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HEADER CELL ADHESION 05-APR-17 5XEQ
TITLE CRYSTAL STRUCTURE OF HUMAN MDGA1 AND HUMAN NEUROLIGIN-2 COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NEUROLIGIN-2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 42-610;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: MAM DOMAIN-CONTAINING GLYCOSYLPHOSPHATIDYLINOSITOL ANCHOR
COMPND 9 PROTEIN 1;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: UNP RESIDUES 19-330;
COMPND 12 SYNONYM: GPI AND MAM PROTEIN,GPIM,GLYCOSYLPHOSPHATIDYLINOSITOL-MAM,
COMPND 13 MAM DOMAIN-CONTAINING PROTEIN 3;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: NLGN2, KIAA1366;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HI5;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PACGP67A;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 GENE: MDGA1, MAMDC3;
SOURCE 16 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 18 EXPRESSION_SYSTEM_STRAIN: HI5;
SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PACGP67A
KEYWDS IMMUNOGLOUBULIN-LIKE DOMAIN, CELL ADHESION
EXPDTA X-RAY DIFFRACTION
AUTHOR H.M.KIM,J.A.KIM,D.KIM
REVDAT 1 12-JUL-17 5XEQ 0
JRNL AUTH J.A.KIM,D.KIM,S.Y.WON,K.A.HAN,D.PARK,E.CHO,N.YUN,H.J.AN,
JRNL AUTH 2 J.W.UM,E.KIM,J.O.LEE,J.KO,H.M.KIM
JRNL TITL STRUCTURAL INSIGHTS INTO MODULATION OF NEUREXIN-NEUROLIGIN
JRNL TITL 2 TRANS-SYNAPTIC ADHESION BY MDGA1/NEUROLIGIN-2 COMPLEX
JRNL REF NEURON V. 94 1121 2017
JRNL REFN ISSN 1097-4199
JRNL PMID 28641111
JRNL DOI 10.1016/J.NEURON.2017.05.034
REMARK 2
REMARK 2 RESOLUTION. 3.14 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10.1_2155
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) : 3.14
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.20
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 18456
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.239
REMARK 3 R VALUE (WORKING SET) : 0.234
REMARK 3 FREE R VALUE : 0.278
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010
REMARK 3 FREE R VALUE TEST SET COUNT : 1847
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 49.2047 - 7.3654 1.00 1336 149 0.2022 0.2101
REMARK 3 2 7.3654 - 5.8492 1.00 1297 144 0.2434 0.2561
REMARK 3 3 5.8492 - 5.1107 1.00 1292 143 0.2207 0.2469
REMARK 3 4 5.1107 - 4.6438 1.00 1286 143 0.2080 0.2695
REMARK 3 5 4.6438 - 4.3112 1.00 1261 140 0.2091 0.2829
REMARK 3 6 4.3112 - 4.0571 1.00 1263 140 0.2211 0.2643
REMARK 3 7 4.0571 - 3.8540 1.00 1263 141 0.2384 0.2906
REMARK 3 8 3.8540 - 3.6863 1.00 1286 143 0.2476 0.3058
REMARK 3 9 3.6863 - 3.5445 1.00 1286 143 0.2757 0.3582
REMARK 3 10 3.5445 - 3.4222 1.00 1279 143 0.2764 0.3549
REMARK 3 11 3.4222 - 3.3152 1.00 1239 138 0.2895 0.3218
REMARK 3 12 3.3152 - 3.2205 1.00 1291 142 0.3012 0.4141
REMARK 3 13 3.2205 - 3.1357 1.00 1230 138 0.3184 0.4017
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) : 0.480
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.350
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 77.18
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.08
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 : 0.004 6618
REMARK 3 ANGLE : 0.680 9024
REMARK 3 CHIRALITY : 0.057 1005
REMARK 3 PLANARITY : 0.004 1176
REMARK 3 DIHEDRAL : 10.957 3928
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
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 5XEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-17.
REMARK 100 THE DEPOSITION ID IS D_1300003400.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-MAY-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 5C (4A)
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18485
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.140
REMARK 200 RESOLUTION RANGE LOW (A) : 49.200
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 12.80
REMARK 200 R MERGE (I) : 0.07500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 22.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.35
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 12.90
REMARK 200 R MERGE FOR SHELL (I) : 0.26100
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: PHASER
REMARK 200 STARTING MODEL: 3BL8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.42
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 300MM AMMONIUM CITRATE TRIBASIC, PH
REMARK 280 7.0, 13% 1,3-BUTANEDIOL AND 18%(V/V) PEG3350, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 296K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 77.43750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.56700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.43750
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.56700
REMARK 290 SMTRY3 4 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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11420 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 68810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -46.53209
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 98.39494
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 ALA A 39
REMARK 465 ASP A 40
REMARK 465 PRO A 41
REMARK 465 THR A 150
REMARK 465 GLU A 151
REMARK 465 ASP A 152
REMARK 465 GLY A 153
REMARK 465 PRO A 154
REMARK 465 LEU A 155
REMARK 465 THR A 156
REMARK 465 LYS A 157
REMARK 465 LYS A 158
REMARK 465 ARG A 159
REMARK 465 ASP A 160
REMARK 465 GLU A 161
REMARK 465 ALA A 162
REMARK 465 THR A 163
REMARK 465 LEU A 164
REMARK 465 ASN A 165
REMARK 465 PRO A 166
REMARK 465 PRO A 167
REMARK 465 ASP A 168
REMARK 465 THR A 169
REMARK 465 ASP A 170
REMARK 465 ILE A 171
REMARK 465 ARG A 172
REMARK 465 ASP A 173
REMARK 465 PRO A 174
REMARK 465 ASP A 393
REMARK 465 SER A 394
REMARK 465 ALA A 395
REMARK 465 GLU A 396
REMARK 465 SER A 397
REMARK 465 GLU A 398
REMARK 465 ASP A 399
REMARK 465 GLY A 400
REMARK 465 GLN A 553
REMARK 465 ASP A 554
REMARK 465 THR A 555
REMARK 465 LYS A 556
REMARK 465 PHE A 557
REMARK 465 ILE A 558
REMARK 465 HIS A 559
REMARK 465 THR A 560
REMARK 465 LYS A 561
REMARK 465 PRO A 562
REMARK 465 ASN A 610
REMARK 465 LEU A 611
REMARK 465 VAL A 612
REMARK 465 PRO A 613
REMARK 465 ARG A 614
REMARK 465 ALA B 16
REMARK 465 ASP B 17
REMARK 465 PRO B 18
REMARK 465 GLN B 19
REMARK 465 GLY B 20
REMARK 465 VAL B 21
REMARK 465 TYR B 22
REMARK 465 ALA B 23
REMARK 465 PRO B 24
REMARK 465 ALA B 25
REMARK 465 ASN B 42
REMARK 465 ILE B 43
REMARK 465 SER B 44
REMARK 465 SER B 80
REMARK 465 ASP B 81
REMARK 465 LYS B 82
REMARK 465 PHE B 83
REMARK 465 GLN B 84
REMARK 465 VAL B 140
REMARK 465 SER B 141
REMARK 465 ASP B 142
REMARK 465 MET B 329
REMARK 465 LYS B 330
REMARK 465 LEU B 331
REMARK 465 VAL B 332
REMARK 465 PRO B 333
REMARK 465 ARG B 334
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O GLU A 386 OG1 THR A 456 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 ASN A 522 CB ASN A 522 CG 0.141
REMARK 500
REMARK 500 REMARK: NULL
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 ASN A 59 41.70 -77.85
REMARK 500 ALA A 113 61.49 66.02
REMARK 500 ASN A 126 52.12 -114.64
REMARK 500 SER A 187 21.93 -153.68
REMARK 500 TYR A 188 -3.52 74.19
REMARK 500 ASP A 226 -164.54 -100.25
REMARK 500 ASN A 248 -14.92 -142.48
REMARK 500 SER A 280 33.54 -98.52
REMARK 500 ASP A 358 -82.43 -113.80
REMARK 500 TYR A 435 57.06 -110.14
REMARK 500 TYR A 474 30.87 -88.24
REMARK 500 GLU A 567 18.73 54.66
REMARK 500 TRP A 570 89.31 -63.08
REMARK 500 GLN B 34 41.72 -98.29
REMARK 500 THR B 75 87.31 -66.78
REMARK 500 ASP B 130 -166.07 -75.55
REMARK 500 GLN B 149 31.95 -92.72
REMARK 500 TYR B 191 14.07 57.99
REMARK 500 TYR B 209 84.81 -67.85
REMARK 500 ASN B 247 -178.41 -68.45
REMARK 500 LEU B 270 108.56 -50.54
REMARK 500 ASN B 313 71.47 -61.70
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG A 701 bound
REMARK 800 to ASN A 522
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG B 403 bound
REMARK 800 to ASN B 235
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG B 404 bound
REMARK 800 to ASN B 257
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG B
REMARK 800 401 through NAG B 402 bound to ASN B 307
DBREF 5XEQ A 42 611 UNP Q8NFZ4 NLGN2_HUMAN 42 611
DBREF 5XEQ B 19 330 UNP Q8NFP4 MDGA1_HUMAN 19 330
SEQADV 5XEQ ALA A 39 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ ASP A 40 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ PRO A 41 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ GLN A 98 UNP Q8NFZ4 ASN 98 ENGINEERED MUTATION
SEQADV 5XEQ VAL A 612 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ PRO A 613 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ ARG A 614 UNP Q8NFZ4 EXPRESSION TAG
SEQADV 5XEQ ALA B 16 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ ASP B 17 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ PRO B 18 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ LEU B 331 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ VAL B 332 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ PRO B 333 UNP Q8NFP4 EXPRESSION TAG
SEQADV 5XEQ ARG B 334 UNP Q8NFP4 EXPRESSION TAG
SEQRES 1 A 576 ALA ASP PRO PRO VAL VAL ASN THR ALA TYR GLY ARG VAL
SEQRES 2 A 576 ARG GLY VAL ARG ARG GLU LEU ASN ASN GLU ILE LEU GLY
SEQRES 3 A 576 PRO VAL VAL GLN PHE LEU GLY VAL PRO TYR ALA THR PRO
SEQRES 4 A 576 PRO LEU GLY ALA ARG ARG PHE GLN PRO PRO GLU ALA PRO
SEQRES 5 A 576 ALA SER TRP PRO GLY VAL ARG GLN ALA THR THR LEU PRO
SEQRES 6 A 576 PRO ALA CYS PRO GLN ASN LEU HIS GLY ALA LEU PRO ALA
SEQRES 7 A 576 ILE MET LEU PRO VAL TRP PHE THR ASP ASN LEU GLU ALA
SEQRES 8 A 576 ALA ALA THR TYR VAL GLN ASN GLN SER GLU ASP CYS LEU
SEQRES 9 A 576 TYR LEU ASN LEU TYR VAL PRO THR GLU ASP GLY PRO LEU
SEQRES 10 A 576 THR LYS LYS ARG ASP GLU ALA THR LEU ASN PRO PRO ASP
SEQRES 11 A 576 THR ASP ILE ARG ASP PRO GLY LYS LYS PRO VAL MET LEU
SEQRES 12 A 576 PHE LEU HIS GLY GLY SER TYR MET GLU GLY THR GLY ASN
SEQRES 13 A 576 MET PHE ASP GLY SER VAL LEU ALA ALA TYR GLY ASN VAL
SEQRES 14 A 576 ILE VAL ALA THR LEU ASN TYR ARG LEU GLY VAL LEU GLY
SEQRES 15 A 576 PHE LEU SER THR GLY ASP GLN ALA ALA LYS GLY ASN TYR
SEQRES 16 A 576 GLY LEU LEU ASP GLN ILE GLN ALA LEU ARG TRP LEU SER
SEQRES 17 A 576 GLU ASN ILE ALA HIS PHE GLY GLY ASP PRO GLU ARG ILE
SEQRES 18 A 576 THR ILE PHE GLY SER GLY ALA GLY ALA SER CYS VAL ASN
SEQRES 19 A 576 LEU LEU ILE LEU SER HIS HIS SER GLU GLY LEU PHE GLN
SEQRES 20 A 576 LYS ALA ILE ALA GLN SER GLY THR ALA ILE SER SER TRP
SEQRES 21 A 576 SER VAL ASN TYR GLN PRO LEU LYS TYR THR ARG LEU LEU
SEQRES 22 A 576 ALA ALA LYS VAL GLY CYS ASP ARG GLU ASP SER ALA GLU
SEQRES 23 A 576 ALA VAL GLU CYS LEU ARG ARG LYS PRO SER ARG GLU LEU
SEQRES 24 A 576 VAL ASP GLN ASP VAL GLN PRO ALA ARG TYR HIS ILE ALA
SEQRES 25 A 576 PHE GLY PRO VAL VAL ASP GLY ASP VAL VAL PRO ASP ASP
SEQRES 26 A 576 PRO GLU ILE LEU MET GLN GLN GLY GLU PHE LEU ASN TYR
SEQRES 27 A 576 ASP MET LEU ILE GLY VAL ASN GLN GLY GLU GLY LEU LYS
SEQRES 28 A 576 PHE VAL GLU ASP SER ALA GLU SER GLU ASP GLY VAL SER
SEQRES 29 A 576 ALA SER ALA PHE ASP PHE THR VAL SER ASN PHE VAL ASP
SEQRES 30 A 576 ASN LEU TYR GLY TYR PRO GLU GLY LYS ASP VAL LEU ARG
SEQRES 31 A 576 GLU THR ILE LYS PHE MET TYR THR ASP TRP ALA ASP ARG
SEQRES 32 A 576 ASP ASN GLY GLU MET ARG ARG LYS THR LEU LEU ALA LEU
SEQRES 33 A 576 PHE THR ASP HIS GLN TRP VAL ALA PRO ALA VAL ALA THR
SEQRES 34 A 576 ALA LYS LEU HIS ALA ASP TYR GLN SER PRO VAL TYR PHE
SEQRES 35 A 576 TYR THR PHE TYR HIS HIS CYS GLN ALA GLU GLY ARG PRO
SEQRES 36 A 576 GLU TRP ALA ASP ALA ALA HIS GLY ASP GLU LEU PRO TYR
SEQRES 37 A 576 VAL PHE GLY VAL PRO MET VAL GLY ALA THR ASP LEU PHE
SEQRES 38 A 576 PRO CYS ASN PHE SER LYS ASN ASP VAL MET LEU SER ALA
SEQRES 39 A 576 VAL VAL MET THR TYR TRP THR ASN PHE ALA LYS THR GLY
SEQRES 40 A 576 ASP PRO ASN GLN PRO VAL PRO GLN ASP THR LYS PHE ILE
SEQRES 41 A 576 HIS THR LYS PRO ASN ARG PHE GLU GLU VAL VAL TRP SER
SEQRES 42 A 576 LYS PHE ASN SER LYS GLU LYS GLN TYR LEU HIS ILE GLY
SEQRES 43 A 576 LEU LYS PRO ARG VAL ARG ASP ASN TYR ARG ALA ASN LYS
SEQRES 44 A 576 VAL ALA PHE TRP LEU GLU LEU VAL PRO HIS LEU HIS ASN
SEQRES 45 A 576 LEU VAL PRO ARG
SEQRES 1 B 319 ALA ASP PRO GLN GLY VAL TYR ALA PRO ALA GLN ALA GLN
SEQRES 2 B 319 ILE VAL HIS ALA GLY GLN ALA CYS VAL VAL LYS GLU ASP
SEQRES 3 B 319 ASN ILE SER GLU ARG VAL TYR THR ILE ARG GLU GLY ASP
SEQRES 4 B 319 THR LEU MET LEU GLN CYS LEU VAL THR GLY HIS PRO ARG
SEQRES 5 B 319 PRO GLN VAL ARG TRP THR LYS THR ALA GLY SER ALA SER
SEQRES 6 B 319 ASP LYS PHE GLN GLU THR SER VAL PHE ASN GLU THR LEU
SEQRES 7 B 319 ARG ILE GLU ARG ILE ALA ARG THR GLN GLY GLY ARG TYR
SEQRES 8 B 319 TYR CYS LYS ALA GLU ASN GLY VAL GLY VAL PRO ALA ILE
SEQRES 9 B 319 LYS SER ILE ARG VAL ASP VAL GLN TYR LEU ASP GLU PRO
SEQRES 10 B 319 MET LEU THR VAL HIS GLN THR VAL SER ASP VAL ARG GLY
SEQRES 11 B 319 ASN PHE TYR GLN GLU LYS THR VAL PHE LEU ARG CYS THR
SEQRES 12 B 319 VAL ASN SER ASN PRO PRO ALA ARG PHE ILE TRP LYS ARG
SEQRES 13 B 319 GLY SER ASP THR LEU SER HIS SER GLN ASP ASN GLY VAL
SEQRES 14 B 319 ASP ILE TYR GLU PRO LEU TYR THR GLN GLY GLU THR LYS
SEQRES 15 B 319 VAL LEU LYS LEU LYS ASN LEU ARG PRO GLN ASP TYR ALA
SEQRES 16 B 319 SER TYR THR CYS GLN VAL SER VAL ARG ASN VAL CYS GLY
SEQRES 17 B 319 ILE PRO ASP LYS ALA ILE THR PHE ARG LEU THR ASN THR
SEQRES 18 B 319 THR ALA PRO PRO ALA LEU LYS LEU SER VAL ASN GLU THR
SEQRES 19 B 319 LEU VAL VAL ASN PRO GLY GLU ASN VAL THR VAL GLN CYS
SEQRES 20 B 319 LEU LEU THR GLY GLY ASP PRO LEU PRO GLN LEU GLN TRP
SEQRES 21 B 319 SER HIS GLY PRO GLY PRO LEU PRO LEU GLY ALA LEU ALA
SEQRES 22 B 319 GLN GLY GLY THR LEU SER ILE PRO SER VAL GLN ALA ARG
SEQRES 23 B 319 ASP SER GLY TYR TYR ASN CYS THR ALA THR ASN ASN VAL
SEQRES 24 B 319 GLY ASN PRO ALA LYS LYS THR VAL ASN LEU LEU VAL ARG
SEQRES 25 B 319 SER MET LYS LEU VAL PRO ARG
HET NAG A 701 14
HET NAG B 401 14
HET NAG B 402 14
HET NAG B 403 14
HET NAG B 404 14
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 3 NAG 5(C8 H15 N O6)
HELIX 1 AA1 PRO A 120 ASN A 126 1 7
HELIX 2 AA2 ASN A 126 THR A 132 1 7
HELIX 3 AA3 TYR A 133 GLN A 135 5 3
HELIX 4 AA4 THR A 192 PHE A 196 5 5
HELIX 5 AA5 GLY A 198 ASN A 206 1 9
HELIX 6 AA6 LEU A 216 LEU A 222 1 7
HELIX 7 AA7 ASN A 232 GLU A 247 1 16
HELIX 8 AA8 ASN A 248 PHE A 252 5 5
HELIX 9 AA9 GLY A 265 SER A 277 1 13
HELIX 10 AB1 GLN A 303 VAL A 315 1 13
HELIX 11 AB2 ASP A 321 ARG A 330 1 10
HELIX 12 AB3 PRO A 333 ASP A 339 1 7
HELIX 13 AB4 ASP A 363 GLN A 370 1 8
HELIX 14 AB5 GLY A 387 GLU A 392 1 6
HELIX 15 AB6 SER A 402 TYR A 418 1 17
HELIX 16 AB7 GLY A 423 TYR A 435 1 13
HELIX 17 AB8 ASN A 443 TRP A 460 1 18
HELIX 18 AB9 TRP A 460 TYR A 474 1 15
HELIX 19 AC1 GLU A 503 PHE A 508 1 6
HELIX 20 AC2 GLY A 509 VAL A 513 5 5
HELIX 21 AC3 SER A 524 GLY A 545 1 22
HELIX 22 AC4 ARG A 594 LEU A 604 1 11
HELIX 23 AC5 ALA B 99 GLY B 103 5 5
HELIX 24 AC6 GLN B 299 SER B 303 5 5
SHEET 1 AA1 3 VAL A 43 ASN A 45 0
SHEET 2 AA1 3 ARG A 50 ARG A 52 -1 O VAL A 51 N VAL A 44
SHEET 3 AA1 3 VAL A 96 GLN A 98 1 O ARG A 97 N ARG A 52
SHEET 1 AA211 VAL A 54 GLU A 57 0
SHEET 2 AA211 PRO A 65 PRO A 73 -1 O GLN A 68 N VAL A 54
SHEET 3 AA211 TYR A 143 VAL A 148 -1 O VAL A 148 N VAL A 67
SHEET 4 AA211 ILE A 208 LEU A 212 -1 O VAL A 209 N TYR A 147
SHEET 5 AA211 LYS A 177 LEU A 183 1 N PHE A 182 O ALA A 210
SHEET 6 AA211 GLY A 254 SER A 264 1 O ASP A 255 N LYS A 177
SHEET 7 AA211 LYS A 286 GLN A 290 1 O GLN A 290 N GLY A 263
SHEET 8 AA211 ASP A 377 ASN A 383 1 O ASP A 377 N ALA A 287
SHEET 9 AA211 VAL A 478 PHE A 483 1 O PHE A 483 N VAL A 382
SHEET 10 AA211 TYR A 580 ILE A 583 1 O LEU A 581 N PHE A 480
SHEET 11 AA211 ARG A 588 ARG A 590 -1 O ARG A 588 N HIS A 582
SHEET 1 AA3 3 GLN B 28 ALA B 32 0
SHEET 2 AA3 3 LEU B 56 THR B 63 -1 O GLN B 59 N ALA B 32
SHEET 3 AA3 3 THR B 92 ILE B 95 -1 O ILE B 95 N LEU B 56
SHEET 1 AA4 4 VAL B 47 ARG B 51 0
SHEET 2 AA4 4 ALA B 118 GLN B 127 1 O ARG B 123 N TYR B 48
SHEET 3 AA4 4 ARG B 105 GLU B 111 -1 N TYR B 106 O ILE B 122
SHEET 4 AA4 4 GLN B 69 LYS B 74 -1 N THR B 73 O TYR B 107
SHEET 1 AA5 4 MET B 133 HIS B 137 0
SHEET 2 AA5 4 VAL B 153 THR B 158 -1 O ARG B 156 N THR B 135
SHEET 3 AA5 4 THR B 196 LEU B 201 -1 O LYS B 197 N CYS B 157
SHEET 4 AA5 4 VAL B 184 TYR B 187 -1 N TYR B 187 O VAL B 198
SHEET 1 AA6 3 ARG B 166 ARG B 171 0
SHEET 2 AA6 3 SER B 211 SER B 217 -1 O SER B 217 N ARG B 166
SHEET 3 AA6 3 LYS B 227 ARG B 232 -1 O PHE B 231 N TYR B 212
SHEET 1 AA7 3 ALA B 241 LEU B 244 0
SHEET 2 AA7 3 VAL B 258 GLY B 266 -1 O LEU B 263 N LYS B 243
SHEET 3 AA7 3 THR B 292 ILE B 295 -1 O LEU B 293 N VAL B 260
SHEET 1 AA8 4 THR B 249 VAL B 252 0
SHEET 2 AA8 4 ALA B 318 VAL B 326 1 O LEU B 325 N LEU B 250
SHEET 3 AA8 4 GLY B 304 THR B 311 -1 N CYS B 308 O LYS B 320
SHEET 4 AA8 4 GLN B 272 GLN B 274 -1 N GLN B 274 O THR B 309
SSBOND 1 CYS A 106 CYS A 141 1555 1555 2.03
SSBOND 2 CYS A 317 CYS A 328 1555 1555 2.03
SSBOND 3 CYS A 487 CYS A 521 1555 1555 2.02
SSBOND 4 CYS B 60 CYS B 108 1555 1555 2.03
SSBOND 5 CYS B 157 CYS B 214 1555 1555 2.03
SSBOND 6 CYS B 262 CYS B 308 1555 1555 2.04
LINK ND2 ASN A 522 C1 NAG A 701 1555 1555 1.52
LINK ND2 ASN B 235 C1 NAG B 403 1555 1555 1.45
LINK ND2 ASN B 257 C1 NAG B 404 1555 1555 1.44
LINK ND2 ASN B 307 C1 NAG B 401 1555 1555 1.46
LINK O4 NAG B 401 C1 NAG B 402 1555 1555 1.46
SITE 1 AC1 3 ASN A 522 PHE A 523 SER A 524
SITE 1 AC2 1 ASN B 235
SITE 1 AC3 1 ASN B 257
SITE 1 AC4 4 GLY B 278 TYR B 305 ASN B 307 LYS B 319
CRYST1 154.875 69.134 108.843 90.00 115.31 90.00 C 1 2 1 4
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 0.006457 0.000000 0.003053 0.00000
SCALE2 0.000000 0.014465 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010163 0.00000
TER 4127 HIS A 609
TER 6382 SER B 328
MASTER 382 0 5 24 35 0 4 6 6450 2 86 70
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