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HEADER HYDROLASE/CELL ADHESION 23-JUN-20 7CEG
TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN MOUSE PTP DELTA AND
TITLE 2 NEUROLIGIN-3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ISOFORM C OF RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE
COMPND 3 DELTA;
COMPND 4 CHAIN: A;
COMPND 5 SYNONYM: R-PTP-DELTA;
COMPND 6 EC: 3.1.3.48;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: NEUROLIGIN-3;
COMPND 10 CHAIN: B;
COMPND 11 SYNONYM: GLIOTACTIN HOMOLOG;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 GENE: PTPRD;
SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F;
SOURCE 9 MOL_ID: 2;
SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 11 ORGANISM_COMMON: MOUSE;
SOURCE 12 ORGANISM_TAXID: 10090;
SOURCE 13 CELL_LINE: HEK293F;
SOURCE 14 GENE: NLGN3;
SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: HEK293F
KEYWDS SYNAPSE ORGANIZATION, TRANS-SYNAPTIC COMPLEX, ESTERASE DOMAIN,
KEYWDS 2 HYDROLASE-CELL ADHESION COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.YAMAGATA,T.YOSHIDA,T.SHIROSHIMA,A.MAEDA,S.FUKAI
REVDAT 1 24-FEB-21 7CEG 0
JRNL AUTH T.YOSHIDA,A.YAMAGATA,A.IMAI,J.KIM,H.IZUMI,S.NAKASHIMA,
JRNL AUTH 2 T.SHIROSHIMA,A.MAEDA,S.IWASAWA-OKAMOTO,K.AZECHI,F.OSAKA,
JRNL AUTH 3 T.SAITOH,K.MAENAKA,T.SHIMADA,Y.FUKATA,M.FUKATA,J.MATSUMOTO,
JRNL AUTH 4 H.NISHIJO,K.TAKAO,S.TANAKA,S.OKABE,K.TABUCHI,T.UEMURA,
JRNL AUTH 5 M.MISHINA,H.MORI,S.FUKAI
JRNL TITL CANONICAL VERSUS NON-CANONICAL TRANSSYNAPTIC SIGNALING OF
JRNL TITL 2 NEUROLIGIN 3 TUNES DEVELOPMENT OF SOCIALITY
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 3.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.69
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 19070
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.255
REMARK 3 R VALUE (WORKING SET) : 0.253
REMARK 3 FREE R VALUE : 0.289
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870
REMARK 3 FREE R VALUE TEST SET COUNT : 928
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 49.6900 - 7.3500 1.00 2716 123 0.2289 0.2560
REMARK 3 2 7.3500 - 5.8400 1.00 2635 140 0.2960 0.3159
REMARK 3 3 5.8400 - 5.1000 1.00 2595 120 0.2526 0.2817
REMARK 3 4 5.1000 - 4.6300 1.00 2593 119 0.2425 0.2887
REMARK 3 5 4.6300 - 4.3000 1.00 2576 139 0.2488 0.3053
REMARK 3 6 4.3000 - 4.0500 1.00 2542 155 0.2753 0.3049
REMARK 3 7 4.0500 - 3.8500 0.98 2485 132 0.3186 0.3789
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.370
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 142.0
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.002 7470
REMARK 3 ANGLE : 0.499 10200
REMARK 3 CHIRALITY : 0.046 1135
REMARK 3 PLANARITY : 0.004 1334
REMARK 3 DIHEDRAL : 14.420 2740
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ( CHAIN B AND RESID 37:363 )
REMARK 3 ORIGIN FOR THE GROUP (A): -3.182 -26.448 -20.500
REMARK 3 T TENSOR
REMARK 3 T11: 1.7922 T22: 1.3063
REMARK 3 T33: 1.1924 T12: 0.2656
REMARK 3 T13: 0.2022 T23: 0.0305
REMARK 3 L TENSOR
REMARK 3 L11: 2.7112 L22: 5.1392
REMARK 3 L33: 1.2705 L12: -0.1218
REMARK 3 L13: -1.0778 L23: 0.3516
REMARK 3 S TENSOR
REMARK 3 S11: -0.1654 S12: -0.8097 S13: 0.0972
REMARK 3 S21: 0.8198 S22: 0.1281 S23: -0.0122
REMARK 3 S31: 0.5338 S32: -0.4108 S33: 0.0677
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN B AND RESID 364:615 )
REMARK 3 ORIGIN FOR THE GROUP (A): -3.206 -32.453 -44.551
REMARK 3 T TENSOR
REMARK 3 T11: 2.5505 T22: 1.2173
REMARK 3 T33: 1.8362 T12: 0.0553
REMARK 3 T13: 0.2948 T23: 0.2908
REMARK 3 L TENSOR
REMARK 3 L11: 2.2876 L22: 1.3620
REMARK 3 L33: 6.4564 L12: 0.3371
REMARK 3 L13: -0.3538 L23: 1.0268
REMARK 3 S TENSOR
REMARK 3 S11: -0.5941 S12: -0.5359 S13: -0.5150
REMARK 3 S21: -0.2083 S22: 0.5669 S23: 0.1165
REMARK 3 S31: 1.2575 S32: -0.8978 S33: 0.0520
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: ( CHAIN A AND RESID 28:137 )
REMARK 3 ORIGIN FOR THE GROUP (A): -3.584 18.028 -26.087
REMARK 3 T TENSOR
REMARK 3 T11: 1.8461 T22: 1.5177
REMARK 3 T33: 1.5094 T12: 0.8020
REMARK 3 T13: 0.0689 T23: -0.2126
REMARK 3 L TENSOR
REMARK 3 L11: 6.2179 L22: 9.2998
REMARK 3 L33: 6.4971 L12: 1.2352
REMARK 3 L13: 4.6120 L23: -3.9398
REMARK 3 S TENSOR
REMARK 3 S11: -0.3444 S12: 0.5542 S13: 0.5045
REMARK 3 S21: -0.0335 S22: 0.1818 S23: -0.3767
REMARK 3 S31: 0.3243 S32: -0.2123 S33: 0.1236
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: ( CHAIN A AND RESID 138:302 )
REMARK 3 ORIGIN FOR THE GROUP (A): 17.409 -13.514 -36.215
REMARK 3 T TENSOR
REMARK 3 T11: 2.0405 T22: 1.2235
REMARK 3 T33: 1.4893 T12: 0.4364
REMARK 3 T13: 0.0036 T23: -0.0807
REMARK 3 L TENSOR
REMARK 3 L11: 4.4620 L22: 5.8760
REMARK 3 L33: 2.6242 L12: -3.9444
REMARK 3 L13: 0.7990 L23: -1.2981
REMARK 3 S TENSOR
REMARK 3 S11: 0.4721 S12: 0.5006 S13: -0.1286
REMARK 3 S21: -0.8657 S22: -0.4673 S23: 0.3437
REMARK 3 S31: -0.0025 S32: 0.6643 S33: -0.0846
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: ( CHAIN A AND RESID 303:413 )
REMARK 3 ORIGIN FOR THE GROUP (A): 43.420 -61.586 -2.804
REMARK 3 T TENSOR
REMARK 3 T11: 2.3267 T22: 1.6662
REMARK 3 T33: 1.7023 T12: 0.9961
REMARK 3 T13: -0.1808 T23: -0.1544
REMARK 3 L TENSOR
REMARK 3 L11: -0.7280 L22: 5.1268
REMARK 3 L33: 3.4283 L12: -0.8863
REMARK 3 L13: 1.3028 L23: -5.0841
REMARK 3 S TENSOR
REMARK 3 S11: 0.1792 S12: -0.1317 S13: 0.9581
REMARK 3 S21: 0.2820 S22: -0.3916 S23: -0.1349
REMARK 3 S31: -0.1407 S32: 0.0903 S33: 0.2147
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7CEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-20.
REMARK 100 THE DEPOSITION ID IS D_1300017474.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19070
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.850
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 8.900
REMARK 200 R MERGE (I) : 0.11900
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 4.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.22
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.30
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
REMARK 200 DATA REDUNDANCY IN SHELL : 5.10
REMARK 200 R MERGE FOR SHELL (I) : 0.33900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 2YD6, 4YFD, 4YFE, 3BIX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 71.28
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1 M AMMONIUM IODIDE,
REMARK 280 0.1 M MES-NA, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -Y,-X,-Z+1/3
REMARK 290 5555 -X+Y,Y,-Z+2/3
REMARK 290 6555 X,X-Y,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 247.74200
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 123.87100
REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 123.87100
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 247.74200
REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4010 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 41630 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLU B 148
REMARK 465 ASP B 149
REMARK 465 GLY B 150
REMARK 465 SER B 151
REMARK 465 GLY B 152
REMARK 465 ALA B 153
REMARK 465 LYS B 154
REMARK 465 LYS B 155
REMARK 465 GLN B 156
REMARK 465 GLY B 157
REMARK 465 GLU B 158
REMARK 465 ASP B 159
REMARK 465 LEU B 160
REMARK 465 ALA B 161
REMARK 465 ASP B 162
REMARK 465 ASN B 163
REMARK 465 ASP B 164
REMARK 465 GLY B 165
REMARK 465 ASP B 166
REMARK 465 GLU B 167
REMARK 465 ASP B 168
REMARK 465 GLU B 169
REMARK 465 ASP B 170
REMARK 465 ILE B 171
REMARK 465 ARG B 172
REMARK 465 ASP B 173
REMARK 465 THR B 555
REMARK 465 LYS B 556
REMARK 465 PHE B 557
REMARK 465 ILE B 558
REMARK 465 HIS B 559
REMARK 465 THR B 560
REMARK 465 LYS B 561
REMARK 465 ALA B 562
REMARK 465 ASN B 563
REMARK 465 ARG B 564
REMARK 465 PHE B 565
REMARK 465 GLU B 566
REMARK 465 GLU B 567
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ARG A 35 88.85 -158.67
REMARK 500 LYS A 67 58.38 -100.03
REMARK 500 SER A 189 -72.07 -68.72
REMARK 500 ALA A 192 -158.81 -142.33
REMARK 500 ASN A 212 -155.61 -131.68
REMARK 500 ARG A 230 70.60 -159.76
REMARK 500 ALA A 270 -48.12 -139.37
REMARK 500 GLU A 276 -44.25 66.99
REMARK 500 ARG A 292 -66.26 -128.32
REMARK 500 PRO A 357 170.06 -58.28
REMARK 500 TYR A 383 57.26 37.35
REMARK 500 ASN A 394 -162.61 -119.53
REMARK 500 GLU B 133 72.04 54.47
REMARK 500 PHE B 221 12.87 -141.89
REMARK 500 ARG B 258 55.16 -113.30
REMARK 500 GLN B 303 54.25 -150.59
REMARK 500 ASP B 358 -70.19 -130.67
REMARK 500 TYR B 420 70.13 51.75
REMARK 500 TYR B 435 51.46 -97.49
REMARK 500 ASP B 440 76.18 -159.51
REMARK 500 TRP B 460 -50.06 -120.46
REMARK 500 ASP B 497 -159.16 -100.25
REMARK 500 LYS B 586 79.63 -116.21
REMARK 500 ARG B 590 -169.51 -121.31
REMARK 500 ASN B 610 59.89 -97.46
REMARK 500 LEU B 611 38.91 -81.94
REMARK 500
REMARK 500 REMARK: NULL
DBREF 7CEG A 28 408 UNP Q64487 PTPRD_MOUSE 21 401
DBREF 7CEG B 37 615 UNP Q8BYM5 NLGN3_MOUSE 37 615
SEQADV 7CEG LYS A 409 UNP Q64487 EXPRESSION TAG
SEQADV 7CEG HIS A 410 UNP Q64487 EXPRESSION TAG
SEQADV 7CEG HIS A 411 UNP Q64487 EXPRESSION TAG
SEQADV 7CEG HIS A 412 UNP Q64487 EXPRESSION TAG
SEQADV 7CEG HIS A 413 UNP Q64487 EXPRESSION TAG
SEQRES 1 A 386 GLU THR PRO PRO ARG PHE THR ARG THR PRO VAL ASP GLN
SEQRES 2 A 386 THR GLY VAL SER GLY GLY VAL ALA SER PHE ILE CYS GLN
SEQRES 3 A 386 ALA THR GLY ASP PRO ARG PRO LYS ILE VAL TRP ASN LYS
SEQRES 4 A 386 LYS GLY LYS LYS VAL SER ASN GLN ARG PHE GLU VAL ILE
SEQRES 5 A 386 GLU PHE ASP ASP GLY SER GLY SER VAL LEU ARG ILE GLN
SEQRES 6 A 386 PRO LEU ARG THR PRO ARG ASP GLU ALA ILE TYR GLU CYS
SEQRES 7 A 386 VAL ALA SER ASN ASN VAL GLY GLU ILE SER VAL SER THR
SEQRES 8 A 386 ARG LEU THR VAL LEU ARG GLU ASP GLN ILE PRO ARG GLY
SEQRES 9 A 386 PHE PRO THR ILE ASP MET GLY PRO GLN LEU LYS VAL VAL
SEQRES 10 A 386 GLU ARG THR ARG THR ALA THR MET LEU CYS ALA ALA SER
SEQRES 11 A 386 GLY ASN PRO ASP PRO GLU ILE THR TRP PHE LYS ASP PHE
SEQRES 12 A 386 LEU PRO VAL ASP THR SER ASN ASN ASN GLY ARG ILE LYS
SEQRES 13 A 386 GLN LEU ARG SER GLU SER ILE GLY ALA LEU GLN ILE GLU
SEQRES 14 A 386 GLN SER GLU GLU SER ASP GLN GLY LYS TYR GLU CYS VAL
SEQRES 15 A 386 ALA THR ASN SER ALA GLY THR ARG TYR SER ALA PRO ALA
SEQRES 16 A 386 ASN LEU TYR VAL ARG VAL ARG ARG VAL PRO PRO ARG PHE
SEQRES 17 A 386 SER ILE PRO PRO THR ASN HIS GLU ILE MET PRO GLY GLY
SEQRES 18 A 386 SER VAL ASN ILE THR CYS VAL ALA VAL GLY SER PRO MET
SEQRES 19 A 386 PRO TYR VAL LYS TRP MET LEU GLY ALA GLU ASP LEU THR
SEQRES 20 A 386 PRO GLU ASP ASP MET PRO ILE GLY ARG ASN VAL LEU GLU
SEQRES 21 A 386 LEU ASN ASP VAL ARG GLN SER ALA ASN TYR THR CYS VAL
SEQRES 22 A 386 ALA MET SER THR LEU GLY VAL ILE GLU ALA ILE ALA GLN
SEQRES 23 A 386 ILE THR VAL LYS ALA LEU PRO LYS PRO PRO GLY THR PRO
SEQRES 24 A 386 VAL VAL THR GLU SER THR ALA THR SER ILE THR LEU THR
SEQRES 25 A 386 TRP ASP SER GLY ASN PRO GLU PRO VAL SER TYR TYR ILE
SEQRES 26 A 386 ILE GLN HIS LYS PRO LYS ASN SER GLU GLU PRO TYR LYS
SEQRES 27 A 386 GLU ILE ASP GLY ILE ALA THR THR ARG TYR SER VAL ALA
SEQRES 28 A 386 GLY LEU SER PRO TYR SER ASP TYR GLU PHE ARG VAL VAL
SEQRES 29 A 386 ALA VAL ASN ASN ILE GLY ARG GLY PRO ALA SER GLU PRO
SEQRES 30 A 386 VAL LEU THR GLN LYS HIS HIS HIS HIS
SEQRES 1 B 579 PRO ALA PRO THR VAL ASN THR HIS PHE GLY LYS LEU ARG
SEQRES 2 B 579 GLY ALA ARG VAL PRO LEU PRO SER GLU ILE LEU GLY PRO
SEQRES 3 B 579 VAL ASP GLN TYR LEU GLY VAL PRO TYR ALA ALA PRO PRO
SEQRES 4 B 579 ILE GLY GLU LYS ARG PHE LEU PRO PRO GLU PRO PRO PRO
SEQRES 5 B 579 SER TRP SER GLY ILE ARG ASN ALA THR HIS PHE PRO PRO
SEQRES 6 B 579 VAL CYS PRO GLN ASN ILE HIS THR ALA VAL PRO GLU VAL
SEQRES 7 B 579 MET LEU PRO VAL TRP PHE THR ALA ASN LEU ASP ILE VAL
SEQRES 8 B 579 ALA THR TYR ILE GLN GLU PRO ASN GLU ASP CYS LEU TYR
SEQRES 9 B 579 LEU ASN VAL TYR VAL PRO THR GLU ASP GLY SER GLY ALA
SEQRES 10 B 579 LYS LYS GLN GLY GLU ASP LEU ALA ASP ASN ASP GLY ASP
SEQRES 11 B 579 GLU ASP GLU ASP ILE ARG ASP SER GLY ALA LYS PRO VAL
SEQRES 12 B 579 MET VAL TYR ILE HIS GLY GLY SER TYR MET GLU GLY THR
SEQRES 13 B 579 GLY ASN MET ILE ASP GLY SER VAL LEU ALA SER TYR GLY
SEQRES 14 B 579 ASN VAL ILE VAL ILE THR LEU ASN TYR ARG VAL GLY VAL
SEQRES 15 B 579 LEU GLY PHE LEU SER THR GLY ASP GLN ALA ALA LYS GLY
SEQRES 16 B 579 ASN TYR GLY LEU LEU ASP GLN ILE GLN ALA LEU ARG TRP
SEQRES 17 B 579 VAL SER GLU ASN ILE ALA PHE PHE GLY GLY ASP PRO ARG
SEQRES 18 B 579 ARG ILE THR VAL PHE GLY SER GLY ILE GLY ALA SER CYS
SEQRES 19 B 579 VAL SER LEU LEU THR LEU SER HIS HIS SER GLU GLY LEU
SEQRES 20 B 579 PHE GLN ARG ALA ILE ILE GLN SER GLY SER ALA LEU SER
SEQRES 21 B 579 SER TRP ALA VAL ASN TYR GLN PRO VAL LYS TYR THR SER
SEQRES 22 B 579 LEU LEU ALA ASP LYS VAL GLY CYS ASN VAL LEU ASP THR
SEQRES 23 B 579 VAL ASP MET VAL ASP CYS LEU ARG GLN LYS SER ALA LYS
SEQRES 24 B 579 GLU LEU VAL GLU GLN ASP ILE GLN PRO ALA ARG TYR HIS
SEQRES 25 B 579 VAL ALA PHE GLY PRO VAL ILE ASP GLY ASP VAL ILE PRO
SEQRES 26 B 579 ASP ASP PRO GLU ILE LEU MET GLU GLN GLY GLU PHE LEU
SEQRES 27 B 579 ASN TYR ASP ILE MET LEU GLY VAL ASN GLN GLY GLU GLY
SEQRES 28 B 579 LEU LYS PHE VAL GLU GLY VAL VAL ASP PRO GLU ASP GLY
SEQRES 29 B 579 VAL SER GLY THR ASP PHE ASP TYR SER VAL SER ASN PHE
SEQRES 30 B 579 VAL ASP ASN LEU TYR GLY TYR PRO GLU GLY LYS ASP THR
SEQRES 31 B 579 LEU ARG GLU THR ILE LYS PHE MET TYR THR ASP TRP ALA
SEQRES 32 B 579 ASP ARG ASP ASN PRO GLU THR ARG ARG LYS THR LEU VAL
SEQRES 33 B 579 ALA LEU PHE THR ASP HIS GLN TRP VAL GLU PRO SER VAL
SEQRES 34 B 579 VAL THR ALA ASP LEU HIS ALA ARG TYR GLY SER PRO THR
SEQRES 35 B 579 TYR PHE TYR ALA PHE TYR HIS HIS CYS GLN SER LEU MET
SEQRES 36 B 579 LYS PRO ALA TRP SER ASP ALA ALA HIS GLY ASP GLU VAL
SEQRES 37 B 579 PRO TYR VAL PHE GLY VAL PRO MET VAL GLY PRO THR ASP
SEQRES 38 B 579 LEU PHE PRO CYS ASN PHE SER LYS ASN ASP VAL MET LEU
SEQRES 39 B 579 SER ALA VAL VAL MET THR TYR TRP THR ASN PHE ALA LYS
SEQRES 40 B 579 THR GLY ASP PRO ASN LYS PRO VAL PRO GLN ASP THR LYS
SEQRES 41 B 579 PHE ILE HIS THR LYS ALA ASN ARG PHE GLU GLU VAL ALA
SEQRES 42 B 579 TRP SER LYS TYR ASN PRO ARG ASP GLN LEU TYR LEU HIS
SEQRES 43 B 579 ILE GLY LEU LYS PRO ARG VAL ARG ASP HIS TYR ARG ALA
SEQRES 44 B 579 THR LYS VAL ALA PHE TRP LYS HIS LEU VAL PRO HIS LEU
SEQRES 45 B 579 TYR ASN LEU HIS ASP MET PHE
HET NAG A 501 14
HET NAG A 502 14
HET NAG B 701 14
HET NAG B 702 14
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA-
HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO-
HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE
FORMUL 3 NAG 4(C8 H15 N O6)
HELIX 1 AA1 GLU A 199 GLN A 203 5 5
HELIX 2 AA2 PRO B 117 ASN B 123 1 7
HELIX 3 AA3 ASN B 123 GLN B 132 1 10
HELIX 4 AA4 THR B 192 ILE B 196 5 5
HELIX 5 AA5 GLY B 198 ASN B 206 1 9
HELIX 6 AA6 GLY B 217 LEU B 222 1 6
HELIX 7 AA7 ASN B 232 ILE B 249 1 18
HELIX 8 AA8 ALA B 250 PHE B 252 5 3
HELIX 9 AA9 ILE B 266 SER B 277 1 12
HELIX 10 AB1 GLN B 303 GLY B 316 1 14
HELIX 11 AB2 ASP B 321 LYS B 332 1 12
HELIX 12 AB3 SER B 333 GLN B 340 1 8
HELIX 13 AB4 ASP B 363 GLN B 370 1 8
HELIX 14 AB5 GLY B 387 GLY B 393 1 7
HELIX 15 AB6 SER B 402 GLY B 419 1 18
HELIX 16 AB7 LYS B 424 TYR B 435 1 12
HELIX 17 AB8 ASN B 443 TRP B 460 1 18
HELIX 18 AB9 TRP B 460 ARG B 473 1 14
HELIX 19 AC1 GLU B 503 GLY B 509 1 7
HELIX 20 AC2 VAL B 510 VAL B 513 5 4
HELIX 21 AC3 SER B 524 GLY B 545 1 22
HELIX 22 AC4 ARG B 594 HIS B 603 1 10
HELIX 23 AC5 HIS B 603 ASN B 610 1 8
HELIX 24 AC6 LEU B 611 PHE B 615 5 5
SHEET 1 AA1 4 THR A 29 ARG A 35 0
SHEET 2 AA1 4 ALA A 48 ASP A 57 -1 O THR A 55 N ARG A 32
SHEET 3 AA1 4 GLY A 86 ILE A 91 -1 O LEU A 89 N PHE A 50
SHEET 4 AA1 4 GLU A 77 GLU A 80 -1 N ILE A 79 O VAL A 88
SHEET 1 AA2 4 GLN A 40 VAL A 43 0
SHEET 2 AA2 4 GLU A 113 LEU A 123 1 O ARG A 119 N GLN A 40
SHEET 3 AA2 4 ILE A 102 SER A 108 -1 N TYR A 103 O THR A 118
SHEET 4 AA2 4 LYS A 61 LYS A 66 -1 N VAL A 63 O VAL A 106
SHEET 1 AA3 2 THR A 134 MET A 137 0
SHEET 2 AA3 2 ALA A 155 SER A 157 -1 O ALA A 155 N MET A 137
SHEET 1 AA4 5 LYS A 142 VAL A 143 0
SHEET 2 AA4 5 ALA A 222 TYR A 225 1 O TYR A 225 N LYS A 142
SHEET 3 AA4 5 GLY A 204 THR A 211 -1 N TYR A 206 O ALA A 222
SHEET 4 AA4 5 GLU A 163 LYS A 168 -1 N PHE A 167 O GLU A 207
SHEET 5 AA4 5 LEU A 171 PRO A 172 -1 O LEU A 171 N LYS A 168
SHEET 1 AA5 4 LYS A 142 VAL A 143 0
SHEET 2 AA5 4 ALA A 222 TYR A 225 1 O TYR A 225 N LYS A 142
SHEET 3 AA5 4 GLY A 204 THR A 211 -1 N TYR A 206 O ALA A 222
SHEET 4 AA5 4 THR A 216 TYR A 218 -1 O ARG A 217 N ALA A 210
SHEET 1 AA6 3 ALA A 150 MET A 152 0
SHEET 2 AA6 3 GLY A 191 ILE A 195 -1 O ILE A 195 N ALA A 150
SHEET 3 AA6 3 ILE A 182 ARG A 186 -1 N LYS A 183 O GLN A 194
SHEET 1 AA7 2 VAL A 231 ILE A 237 0
SHEET 2 AA7 2 VAL A 255 SER A 259 -1 O VAL A 257 N ARG A 234
SHEET 1 AA8 2 VAL A 250 ILE A 252 0
SHEET 2 AA8 2 LEU A 286 LEU A 288 -1 O LEU A 286 N ILE A 252
SHEET 1 AA9 3 TYR A 263 MET A 267 0
SHEET 2 AA9 3 ALA A 295 MET A 302 -1 O VAL A 300 N LYS A 265
SHEET 3 AA9 3 VAL A 307 ILE A 314 -1 O ALA A 312 N TYR A 297
SHEET 1 AB1 3 VAL A 327 SER A 331 0
SHEET 2 AB1 3 SER A 335 THR A 339 -1 O THR A 337 N THR A 329
SHEET 3 AB1 3 ARG A 374 ALA A 378 -1 O VAL A 377 N ILE A 336
SHEET 1 AB2 4 LYS A 365 ILE A 370 0
SHEET 2 AB2 4 TYR A 350 PRO A 357 -1 N ILE A 353 O ILE A 367
SHEET 3 AB2 4 TYR A 386 VAL A 393 -1 O ARG A 389 N GLN A 354
SHEET 4 AB2 4 ARG A 398 ALA A 401 -1 O GLY A 399 N ALA A 392
SHEET 1 AB3 4 LYS A 365 ILE A 370 0
SHEET 2 AB3 4 TYR A 350 PRO A 357 -1 N ILE A 353 O ILE A 367
SHEET 3 AB3 4 TYR A 386 VAL A 393 -1 O ARG A 389 N GLN A 354
SHEET 4 AB3 4 VAL A 405 LEU A 406 -1 O VAL A 405 N PHE A 388
SHEET 1 AB4 3 THR B 40 THR B 43 0
SHEET 2 AB4 3 GLY B 46 ARG B 49 -1 O LEU B 48 N VAL B 41
SHEET 3 AB4 3 ILE B 93 ASN B 95 1 O ARG B 94 N LYS B 47
SHEET 1 AB511 ALA B 51 VAL B 53 0
SHEET 2 AB511 VAL B 63 PRO B 70 -1 O VAL B 63 N VAL B 53
SHEET 3 AB511 TYR B 140 PRO B 146 -1 O VAL B 145 N ASP B 64
SHEET 4 AB511 ILE B 208 LEU B 212 -1 O THR B 211 N ASN B 142
SHEET 5 AB511 LYS B 177 GLY B 185 1 N MET B 180 O ILE B 208
SHEET 6 AB511 GLY B 254 GLY B 265 1 O PHE B 262 N VAL B 181
SHEET 7 AB511 ARG B 286 GLN B 290 1 O GLN B 290 N GLY B 265
SHEET 8 AB511 ASP B 377 ASN B 383 1 O MET B 379 N ILE B 289
SHEET 9 AB511 THR B 478 PHE B 483 1 O PHE B 483 N VAL B 382
SHEET 10 AB511 LEU B 579 ILE B 583 1 O ILE B 583 N ALA B 482
SHEET 11 AB511 ARG B 588 ASP B 591 -1 O ARG B 588 N HIS B 582
SSBOND 1 CYS A 52 CYS A 105 1555 1555 2.03
SSBOND 2 CYS A 154 CYS A 208 1555 1555 2.03
SSBOND 3 CYS A 254 CYS A 299 1555 1555 2.04
SSBOND 4 CYS B 103 CYS B 138 1555 1555 2.03
SSBOND 5 CYS B 317 CYS B 328 1555 1555 2.04
SSBOND 6 CYS B 487 CYS B 521 1555 1555 2.03
LINK ND2 ASN A 251 C1 NAG A 502 1555 1555 1.45
LINK ND2 ASN A 296 C1 NAG A 501 1555 1555 1.44
LINK ND2 ASN B 95 C1 NAG B 701 1555 1555 1.44
LINK ND2 ASN B 522 C1 NAG B 702 1555 1555 1.45
CISPEP 1 ASP A 57 PRO A 58 0 1.67
CISPEP 2 GLN A 92 PRO A 93 0 -3.90
CISPEP 3 THR A 96 PRO A 97 0 -5.67
CISPEP 4 ASN A 159 PRO A 160 0 2.66
CISPEP 5 SER A 259 PRO A 260 0 -0.20
CISPEP 6 LYS B 549 PRO B 550 0 3.10
CRYST1 96.109 96.109 371.613 90.00 90.00 120.00 P 32 1 2 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.010405 0.006007 0.000000 0.00000
SCALE2 0.000000 0.012014 0.000000 0.00000
SCALE3 0.000000 0.000000 0.002691 0.00000
TER 2976 HIS A 413
TER 7219 PHE B 615
MASTER 371 0 4 24 54 0 0 6 7273 2 72 75
END |