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HEADER SIGNALING PROTEIN 29-JUL-10 2XMR
TITLE CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS
TITLE 2 ROLE AS A TUMOR SUPPRESSOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN NDRG2;
COMPND 3 CHAIN: A, B, C;
COMPND 4 FRAGMENT: ALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304;
COMPND 5 SYNONYM: NDRG2;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS SIGNALING PROTEIN, NDRG FAMILY
EXPDTA X-RAY DIFFRACTION
AUTHOR J.HWANG,Y.KIM,H.LEE,M.H.KIM
REVDAT 1 19-JAN-11 2XMR 0
JRNL AUTH J.HWANG,Y.KIM,H.LEE,M.H.KIM
JRNL TITL CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
JRNL TITL 2 INTO ITS ROLE AS A TUMOR SUPPRESSOR
JRNL REF J.BIOL.CHEM. 2011
JRNL REFN ESSN 1083-351X
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.45
REMARK 3 NUMBER OF REFLECTIONS : 60071
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.18282
REMARK 3 R VALUE (WORKING SET) : 0.18019
REMARK 3 FREE R VALUE : 0.23247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1
REMARK 3 FREE R VALUE TEST SET COUNT : 3217
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.003
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.055
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4075
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.87
REMARK 3 BIN R VALUE (WORKING SET) : 0.261
REMARK 3 BIN FREE R VALUE SET COUNT : 219
REMARK 3 BIN FREE R VALUE : 0.357
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6602
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 31
REMARK 3 SOLVENT ATOMS : 399
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 0
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.606
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.45
REMARK 3 B22 (A**2) : -0.10
REMARK 3 B33 (A**2) : 0.55
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.174
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.335
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6801 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9263 ; 1.342 ; 1.962
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 842 ; 8.966 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;36.103 ;24.921
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1064 ;15.297 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.423 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1008 ; 0.089 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5291 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3013 ; 0.205 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4656 ; 0.310 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 398 ; 0.154 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 64 ; 0.206 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.276 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4318 ; 0.760 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6812 ; 1.245 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2819 ; 1.845 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2451 ; 2.900 ; 4.500
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 2XMR COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-10.
REMARK 100 THE PDBE ID CODE IS EBI-44856.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 6C1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.23985
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63329
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00
REMARK 200 RESOLUTION RANGE LOW (A) : 30.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 200 DATA REDUNDANCY : 4.6
REMARK 200 R MERGE (I) : 0.14
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 11.27
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2
REMARK 200 DATA REDUNDANCY IN SHELL : 3.1
REMARK 200 R MERGE FOR SHELL (I) : 0.44
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 1.83
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: PDB ENTRY 2QMQ
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 0.2 M CALCIUM ACETATE,
REMARK 280 0.1 M MES (PH 6.8 TO 7.1)
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 43.11600
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.45350
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.02450
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.45350
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.11600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.02450
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2, 3
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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
REMARK 350 BIOMOLECULE: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
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 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 45 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 47 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 45 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 47 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN C, LYS 45 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN C, LYS 47 TO ALA
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 N ALA C 47 O HOH C 2007 2.16
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 230 32.52 75.15
REMARK 500 GLN B 285 57.35 -140.79
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 TYR A 223 ASN A 224 -144.25
REMARK 500 ASN A 224 ASN A 225 -142.88
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A1305 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 47 O
REMARK 620 2 TYR C 302 OH 82.6
REMARK 620 3 HOH A2067 O 91.4 159.2
REMARK 620 4 TYR A 302 OH 93.9 120.6 79.6
REMARK 620 5 HOH C2054 O 96.8 78.3 82.6 159.4
REMARK 620 6 ALA C 47 O 174.5 91.9 93.7 88.9 82.0
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C1306
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1307
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2XMS RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
REMARK 900 INTO ITS ROLE AS A TUMOR SUPPRESSOR
REMARK 900 RELATED ID: 2XMQ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT
REMARK 900 INTO ITS ROLE AS A TUMOR SUPPRESSOR
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 MUTANT OF PDB ID 2XMQ
DBREF 2XMR A 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
DBREF 2XMR B 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
DBREF 2XMR C 24 304 UNP Q9UN36 NDRG2_HUMAN 24 304
SEQADV 2XMR ALA A 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION
SEQADV 2XMR ALA A 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION
SEQADV 2XMR ALA B 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION
SEQADV 2XMR ALA B 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION
SEQADV 2XMR ALA C 45 UNP Q9UN36 LYS 45 ENGINEERED MUTATION
SEQADV 2XMR ALA C 47 UNP Q9UN36 LYS 47 ENGINEERED MUTATION
SEQRES 1 A 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 A 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO
SEQRES 3 A 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 A 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 A 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 A 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 A 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 A 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 A 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 A 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 A 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 A 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 A 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 A 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 A 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU
SEQRES 16 A 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 A 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 A 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 A 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 A 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 A 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 A 281 LEU GLN GLY MET GLY TYR MET ALA
SEQRES 1 B 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 B 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO
SEQRES 3 B 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 B 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 B 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 B 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 B 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 B 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 B 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 B 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 B 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 B 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 B 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 B 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 B 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU
SEQRES 16 B 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 B 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 B 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 B 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 B 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 B 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 B 281 LEU GLN GLY MET GLY TYR MET ALA
SEQRES 1 C 281 ALA LYS THR HIS SER VAL GLU THR PRO TYR GLY SER VAL
SEQRES 2 C 281 THR PHE THR VAL TYR GLY THR PRO ALA PRO ALA ARG PRO
SEQRES 3 C 281 ALA ILE LEU THR TYR HIS ASP VAL GLY LEU ASN TYR LYS
SEQRES 4 C 281 SER CYS PHE GLN PRO LEU PHE GLN PHE GLU ASP MET GLN
SEQRES 5 C 281 GLU ILE ILE GLN ASN PHE VAL ARG VAL HIS VAL ASP ALA
SEQRES 6 C 281 PRO GLY MET GLU GLU GLY ALA PRO VAL PHE PRO LEU GLY
SEQRES 7 C 281 TYR GLN TYR PRO SER LEU ASP GLN LEU ALA ASP MET ILE
SEQRES 8 C 281 PRO CYS VAL LEU GLN TYR LEU ASN PHE SER THR ILE ILE
SEQRES 9 C 281 GLY VAL GLY VAL GLY ALA GLY ALA TYR ILE LEU ALA ARG
SEQRES 10 C 281 TYR ALA LEU ASN HIS PRO ASP THR VAL GLU GLY LEU VAL
SEQRES 11 C 281 LEU ILE ASN ILE ASP PRO ASN ALA LYS GLY TRP MET ASP
SEQRES 12 C 281 TRP ALA ALA HIS LYS LEU THR GLY LEU THR SER SER ILE
SEQRES 13 C 281 PRO GLU MET ILE LEU GLY HIS LEU PHE SER GLN GLU GLU
SEQRES 14 C 281 LEU SER GLY ASN SER GLU LEU ILE GLN LYS TYR ARG ASN
SEQRES 15 C 281 ILE ILE THR HIS ALA PRO ASN LEU ASP ASN ILE GLU LEU
SEQRES 16 C 281 TYR TRP ASN SER TYR ASN ASN ARG ARG ASP LEU ASN PHE
SEQRES 17 C 281 GLU ARG GLY GLY ASP ILE THR LEU ARG CYS PRO VAL MET
SEQRES 18 C 281 LEU VAL VAL GLY ASP GLN ALA PRO HIS GLU ASP ALA VAL
SEQRES 19 C 281 VAL GLU CYS ASN SER LYS LEU ASP PRO THR GLN THR SER
SEQRES 20 C 281 PHE LEU LYS MET ALA ASP SER GLY GLY GLN PRO GLN LEU
SEQRES 21 C 281 THR GLN PRO GLY LYS LEU THR GLU ALA PHE LYS TYR PHE
SEQRES 22 C 281 LEU GLN GLY MET GLY TYR MET ALA
HET CA A1305 1
HET ACT A1306 4
HET GOL A1307 6
HET ACT B1305 4
HET GOL B1306 6
HET ACT C1305 4
HET GOL C1306 6
HETNAM CA CALCIUM ION
HETNAM ACT ACETATE ION
HETNAM GOL GLYCEROL
FORMUL 4 CA CA 2+
FORMUL 5 ACT 3(C2 H3 O2 1-)
FORMUL 6 GOL 3(C3 H8 O3)
FORMUL 7 HOH *399(H2 O)
HELIX 1 1 ASN A 60 PHE A 65 1 6
HELIX 2 2 PHE A 65 PHE A 71 1 7
HELIX 3 3 PHE A 71 GLN A 79 1 9
HELIX 4 4 SER A 106 ASP A 112 1 7
HELIX 5 5 MET A 113 ASN A 122 1 10
HELIX 6 6 GLY A 132 HIS A 145 1 14
HELIX 7 7 GLY A 163 GLY A 174 1 12
HELIX 8 8 SER A 178 PHE A 188 1 11
HELIX 9 9 SER A 189 ASN A 196 1 8
HELIX 10 10 SER A 197 HIS A 209 1 13
HELIX 11 11 ASN A 212 ASN A 225 1 14
HELIX 12 12 HIS A 253 SER A 262 1 10
HELIX 13 13 GLN A 280 GLN A 285 1 6
HELIX 14 14 GLN A 285 GLY A 301 1 17
HELIX 15 15 ASN B 60 PHE B 65 1 6
HELIX 16 16 PHE B 65 PHE B 71 1 7
HELIX 17 17 PHE B 71 GLN B 79 1 9
HELIX 18 18 SER B 106 ASP B 112 1 7
HELIX 19 19 MET B 113 ASN B 122 1 10
HELIX 20 20 GLY B 132 HIS B 145 1 14
HELIX 21 21 GLY B 163 GLY B 174 1 12
HELIX 22 22 SER B 178 PHE B 188 1 11
HELIX 23 23 SER B 189 ASN B 196 1 8
HELIX 24 24 SER B 197 HIS B 209 1 13
HELIX 25 25 ASN B 212 ASN B 225 1 14
HELIX 26 26 HIS B 253 LEU B 264 1 12
HELIX 27 27 GLN B 280 GLN B 285 1 6
HELIX 28 28 GLN B 285 MET B 300 1 16
HELIX 29 29 ASN C 60 PHE C 65 1 6
HELIX 30 30 PHE C 65 GLN C 70 1 6
HELIX 31 31 PHE C 71 GLN C 79 1 9
HELIX 32 32 SER C 106 ASP C 112 1 7
HELIX 33 33 MET C 113 ASN C 122 1 10
HELIX 34 34 GLY C 132 HIS C 145 1 14
HELIX 35 35 GLY C 163 GLY C 174 1 12
HELIX 36 36 SER C 178 PHE C 188 1 11
HELIX 37 37 SER C 189 ASN C 196 1 8
HELIX 38 38 SER C 197 HIS C 209 1 13
HELIX 39 39 ASN C 212 ARG C 226 1 15
HELIX 40 40 HIS C 253 LEU C 264 1 12
HELIX 41 41 GLN C 280 GLN C 285 1 6
HELIX 42 42 GLN C 285 MET C 300 1 16
SHEET 1 AA 8 LYS A 25 THR A 31 0
SHEET 2 AA 8 GLY A 34 TYR A 41 -1 O GLY A 34 N THR A 31
SHEET 3 AA 8 ARG A 83 ASP A 87 -1 O ARG A 83 N TYR A 41
SHEET 4 AA 8 ALA A 50 TYR A 54 1 O ILE A 51 N VAL A 84
SHEET 5 AA 8 ILE A 126 VAL A 131 1 O ILE A 127 N LEU A 52
SHEET 6 AA 8 VAL A 149 ILE A 155 1 N GLU A 150 O ILE A 126
SHEET 7 AA 8 VAL A 243 GLY A 248 1 O MET A 244 N LEU A 154
SHEET 8 AA 8 THR A 269 MET A 274 1 O SER A 270 N LEU A 245
SHEET 1 BA 8 LYS B 25 THR B 31 0
SHEET 2 BA 8 GLY B 34 TYR B 41 -1 O GLY B 34 N THR B 31
SHEET 3 BA 8 ARG B 83 ASP B 87 -1 O ARG B 83 N TYR B 41
SHEET 4 BA 8 ALA B 50 TYR B 54 1 O ILE B 51 N VAL B 84
SHEET 5 BA 8 ILE B 126 VAL B 131 1 O ILE B 127 N LEU B 52
SHEET 6 BA 8 VAL B 149 ILE B 155 1 N GLU B 150 O ILE B 126
SHEET 7 BA 8 VAL B 243 GLY B 248 1 O MET B 244 N LEU B 154
SHEET 8 BA 8 THR B 269 MET B 274 1 O SER B 270 N LEU B 245
SHEET 1 CA 8 LYS C 25 THR C 31 0
SHEET 2 CA 8 GLY C 34 TYR C 41 -1 O GLY C 34 N THR C 31
SHEET 3 CA 8 ARG C 83 ASP C 87 -1 O ARG C 83 N TYR C 41
SHEET 4 CA 8 ALA C 50 TYR C 54 1 O ILE C 51 N VAL C 84
SHEET 5 CA 8 ILE C 126 VAL C 131 1 O ILE C 127 N LEU C 52
SHEET 6 CA 8 VAL C 149 ILE C 155 1 N GLU C 150 O ILE C 126
SHEET 7 CA 8 VAL C 243 GLY C 248 1 O MET C 244 N LEU C 154
SHEET 8 CA 8 THR C 269 MET C 274 1 O SER C 270 N LEU C 245
LINK CA CA A1305 O ALA A 47 1555 1555 2.65
LINK CA CA A1305 OH TYR C 302 1555 3554 2.95
LINK CA CA A1305 O HOH A2067 1555 1555 2.79
LINK CA CA A1305 OH TYR A 302 1555 1555 2.85
LINK CA CA A1305 O HOH C2054 1555 3554 2.85
LINK CA CA A1305 O ALA C 47 1555 3554 2.77
SITE 1 AC1 6 ALA A 47 TYR A 302 HOH A2067 ALA C 47
SITE 2 AC1 6 TYR C 302 HOH C2054
SITE 1 AC2 5 TYR B 41 TYR B 61 GLN B 75 ARG B 83
SITE 2 AC2 5 HIS B 85
SITE 1 AC3 7 TYR C 41 TYR C 61 PHE C 69 GLN C 75
SITE 2 AC3 7 ARG C 83 HIS C 85 HOH C2115
SITE 1 AC4 6 TYR A 61 GLN A 75 ILE A 78 ARG A 83
SITE 2 AC4 6 HIS A 85 HOH A2132
SITE 1 AC5 7 GLY B 58 LEU B 59 ASN B 60 SER B 63
SITE 2 AC5 7 MET B 91 ILE B 206 ASN B 212
SITE 1 AC6 8 GLY C 58 LEU C 59 ASN C 60 SER C 63
SITE 2 AC6 8 MET C 91 ILE C 206 ALA C 210 ASN C 212
SITE 1 AC7 8 GLY A 58 LEU A 59 ASN A 60 SER A 63
SITE 2 AC7 8 MET A 91 ILE A 206 ALA A 210 ASN A 212
CRYST1 86.232 88.049 126.907 90.00 90.00 90.00 P 21 21 21 12
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 0.011597 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011357 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007880 0.00000
TER 2198 ALA A 304
TER 4396 ALA B 304
TER 6605 ALA C 304
MASTER 353 0 7 42 24 0 14 6 7032 3 34 66
END |