HEADER TRANSFERASE 11-MAY-10 2XE7
TITLE THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN
TITLE 2 TERNARY COMPLEX WITH 3PG AND ADP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PRIMER RECOGNITION PROTEIN 2, PRP 2, CELL MIGRATION-INDUCING
COMPND 5 GENE 10 PROTEIN;
COMPND 6 EC: 2.7.2.3;
COMPND 7 ENGINEERED: 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: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22A
KEYWDS TRANSITION STATE ANALOGUE, HEREDITARY HEMOLYTIC ANEMIA,
KEYWDS 2 PHOSPHOPROTEIN, GLYCOLYSIS, TRANSFERASE, PHOSPHORYL TRANSFER,
KEYWDS 3 NUCLEOTIDE-BINDING, DOMAIN MOTIONS
EXPDTA X-RAY DIFFRACTION
AUTHOR M.J.CLIFF,N.J.BAXTER,G.M.BLACKBURN,A.MERLI,M.VAS,J.P.WALTHO,
AUTHOR 2 M.W.BOWLER
REVDAT 4 20-DEC-23 2XE7 1 REMARK
REVDAT 3 26-OCT-11 2XE7 1 JRNL REMARK VERSN
REVDAT 2 27-APR-11 2XE7 1 JRNL REMARK
REVDAT 1 19-JAN-11 2XE7 0
JRNL AUTH L.ZERRAD,A.MERLI,G.F.SCHRODER,A.VARGA,E.GRACZER,P.PERNOT,
JRNL AUTH 2 A.ROUND,M.VAS,M.W.BOWLER
JRNL TITL A SPRING LOADED RELEASE MECHANISM REGULATES DOMAIN MOVEMENT
JRNL TITL 2 AND CATALYSIS IN PHOSPHOGLYCERATE KINASE.
JRNL REF J.BIOL.CHEM. V. 286 14040 2011
JRNL REFN ISSN 0021-9258
JRNL PMID 21349853
JRNL DOI 10.1074/JBC.M110.206813
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 19766
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) : 0.228
REMARK 3 R VALUE (WORKING SET) : 0.224
REMARK 3 FREE R VALUE : 0.288
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1050
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1441
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87
REMARK 3 BIN R VALUE (WORKING SET) : 0.3020
REMARK 3 BIN FREE R VALUE SET COUNT : 88
REMARK 3 BIN FREE R VALUE : 0.3750
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3096
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 38
REMARK 3 SOLVENT ATOMS : 64
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 32.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.51000
REMARK 3 B22 (A**2) : 0.99000
REMARK 3 B33 (A**2) : -2.51000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.347
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.231
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.949
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3216 ; 0.017 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2190 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4337 ; 1.621 ; 1.992
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5405 ; 0.915 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 6.690 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;42.565 ;25.785
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 586 ;17.940 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.393 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.082 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3525 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 573 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 2060 ; 0.673 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 857 ; 0.162 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3293 ; 1.217 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1156 ; 2.081 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1043 ; 3.259 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 4 A 186
REMARK 3 ORIGIN FOR THE GROUP (A): 13.5880 -20.1510 -33.6130
REMARK 3 T TENSOR
REMARK 3 T11: 0.0925 T22: 0.3252
REMARK 3 T33: 0.0029 T12: -0.1807
REMARK 3 T13: -0.0301 T23: 0.0462
REMARK 3 L TENSOR
REMARK 3 L11: 3.1756 L22: 3.3453
REMARK 3 L33: 4.7110 L12: 0.3730
REMARK 3 L13: 0.9744 L23: 0.1785
REMARK 3 S TENSOR
REMARK 3 S11: -0.0825 S12: 0.6285 S13: 0.1308
REMARK 3 S21: -0.0960 S22: 0.1399 S23: 0.0098
REMARK 3 S31: -0.5616 S32: 0.6635 S33: -0.0574
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
REMARK 4
REMARK 4 2XE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-10.
REMARK 100 THE DEPOSITION ID IS D_1290043895.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-JUN-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.933
REMARK 200 MONOCHROMATOR : DIAMOND 110
REMARK 200 OPTICS : GE 221
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20841
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.29000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
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 3C39
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 100MM TRIS PH 8.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
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 29.31000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.72500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.31000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.72500
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: 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 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 MET A 0
REMARK 465 SER A 1
REMARK 465 LEU A 2
REMARK 465 SER A 3
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 LYS A 55 O ALA A 111 1.94
REMARK 500 OE2 GLU A 343 O2' ADP A 1418 2.13
REMARK 500 ND2 ASN A 137 O HOH A 2020 2.18
REMARK 500 O VAL A 13 CG LYS A 16 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 CB ALA A 308 CB ALA A 308 2445 1.63
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 GLN A 32 N GLN A 32 CA -0.134
REMARK 500 TYR A 75 CD1 TYR A 75 CE1 -0.104
REMARK 500 TYR A 75 CE2 TYR A 75 CD2 -0.107
REMARK 500 CYS A 98 CB CYS A 98 SG -0.103
REMARK 500 ASP A 218 N ASP A 218 CA -0.173
REMARK 500 ASP A 218 N ASP A 218 CA -0.277
REMARK 500 CYS A 315 CB CYS A 315 SG -0.128
REMARK 500 CYS A 378 CB CYS A 378 SG -0.145
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
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 ATM2 ATM3
REMARK 500 PRO A 110 C - N - CD ANGL. DEV. = -14.7 DEGREES
REMARK 500 GLY A 212 CA - C - N ANGL. DEV. = 12.9 DEGREES
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 109 79.90 -153.24
REMARK 500 PRO A 110 -166.47 -68.25
REMARK 500 ALA A 214 -73.78 -89.30
REMARK 500 LYS A 215 52.61 106.69
REMARK 500 ILE A 220 -63.76 -137.66
REMARK 500 PRO A 307 164.37 -44.94
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 RESIDUE 3PG A 1417
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1418
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2X15 RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 1,3-
REMARK 900 BISPHOSPHOGLYCERATE
REMARK 900 RELATED ID: 2WZD RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH ADP, 3PG AND
REMARK 900 ALUMINIUM TRIFLUORIDE
REMARK 900 RELATED ID: 2X14 RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH AMP-PCP AND 3PG
REMARK 900 RELATED ID: 2X13 RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 3PHOSPHOGLYCERATE
REMARK 900 RELATED ID: 2WZB RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND MAGNESIUM
REMARK 900 TRIFLUORIDE
REMARK 900 RELATED ID: 2WZC RELATED DB: PDB
REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND ALUMINIUM
REMARK 900 TETRAFLUORIDE
REMARK 900 RELATED ID: 2XE6 RELATED DB: PDB
REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE
REMARK 900 OPEN BINARY COMPLEX WITH 3PG
REMARK 900 RELATED ID: 2XE8 RELATED DB: PDB
REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE
REMARK 900 OPEN TERNARY COMPLEX WITH 3PG AND AMP-PNP
DBREF 2XE7 A 0 416 UNP P00558 PGK1_HUMAN 1 417
SEQRES 1 A 417 MET SER LEU SER ASN LYS LEU THR LEU ASP LYS LEU ASP
SEQRES 2 A 417 VAL LYS GLY LYS ARG VAL VAL MET ARG VAL ASP PHE ASN
SEQRES 3 A 417 VAL PRO MET LYS ASN ASN GLN ILE THR ASN ASN GLN ARG
SEQRES 4 A 417 ILE LYS ALA ALA VAL PRO SER ILE LYS PHE CYS LEU ASP
SEQRES 5 A 417 ASN GLY ALA LYS SER VAL VAL LEU MET SER HIS LEU GLY
SEQRES 6 A 417 ARG PRO ASP GLY VAL PRO MET PRO ASP LYS TYR SER LEU
SEQRES 7 A 417 GLU PRO VAL ALA VAL GLU LEU LYS SER LEU LEU GLY LYS
SEQRES 8 A 417 ASP VAL LEU PHE LEU LYS ASP CYS VAL GLY PRO GLU VAL
SEQRES 9 A 417 GLU LYS ALA CYS ALA ASN PRO ALA ALA GLY SER VAL ILE
SEQRES 10 A 417 LEU LEU GLU ASN LEU ARG PHE HIS VAL GLU GLU GLU GLY
SEQRES 11 A 417 LYS GLY LYS ASP ALA SER GLY ASN LYS VAL LYS ALA GLU
SEQRES 12 A 417 PRO ALA LYS ILE GLU ALA PHE ARG ALA SER LEU SER LYS
SEQRES 13 A 417 LEU GLY ASP VAL TYR VAL ASN ASP ALA PHE GLY THR ALA
SEQRES 14 A 417 HIS ARG ALA HIS SER SER MET VAL GLY VAL ASN LEU PRO
SEQRES 15 A 417 GLN LYS ALA GLY GLY PHE LEU MET LYS LYS GLU LEU ASN
SEQRES 16 A 417 TYR PHE ALA LYS ALA LEU GLU SER PRO GLU ARG PRO PHE
SEQRES 17 A 417 LEU ALA ILE LEU GLY GLY ALA LYS VAL ALA ASP LYS ILE
SEQRES 18 A 417 GLN LEU ILE ASN ASN MET LEU ASP LYS VAL ASN GLU MET
SEQRES 19 A 417 ILE ILE GLY GLY GLY MET ALA PHE THR PHE LEU LYS VAL
SEQRES 20 A 417 LEU ASN ASN MET GLU ILE GLY THR SER LEU PHE ASP GLU
SEQRES 21 A 417 GLU GLY ALA LYS ILE VAL LYS ASP LEU MET SER LYS ALA
SEQRES 22 A 417 GLU LYS ASN GLY VAL LYS ILE THR LEU PRO VAL ASP PHE
SEQRES 23 A 417 VAL THR ALA ASP LYS PHE ASP GLU ASN ALA LYS THR GLY
SEQRES 24 A 417 GLN ALA THR VAL ALA SER GLY ILE PRO ALA GLY TRP MET
SEQRES 25 A 417 GLY LEU ASP CYS GLY PRO GLU SER SER LYS LYS TYR ALA
SEQRES 26 A 417 GLU ALA VAL THR ARG ALA LYS GLN ILE VAL TRP ASN GLY
SEQRES 27 A 417 PRO VAL GLY VAL PHE GLU TRP GLU ALA PHE ALA ARG GLY
SEQRES 28 A 417 THR LYS ALA LEU MET ASP GLU VAL VAL LYS ALA THR SER
SEQRES 29 A 417 ARG GLY CYS ILE THR ILE ILE GLY GLY GLY ASP THR ALA
SEQRES 30 A 417 THR CYS CYS ALA LYS TRP ASN THR GLU ASP LYS VAL SER
SEQRES 31 A 417 HIS VAL SER THR GLY GLY GLY ALA SER LEU GLU LEU LEU
SEQRES 32 A 417 GLU GLY LYS VAL LEU PRO GLY VAL ASP ALA LEU SER ASN
SEQRES 33 A 417 ILE
HET 3PG A1417 11
HET ADP A1418 27
HETNAM 3PG 3-PHOSPHOGLYCERIC ACID
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
FORMUL 2 3PG C3 H7 O7 P
FORMUL 3 ADP C10 H15 N5 O10 P2
FORMUL 4 HOH *64(H2 O)
HELIX 1 1 LEU A 8 LEU A 11 5 4
HELIX 2 2 ASN A 36 ALA A 41 1 6
HELIX 3 3 ALA A 42 ASN A 52 1 11
HELIX 4 4 LEU A 77 GLY A 89 1 13
HELIX 5 5 GLY A 100 ALA A 108 1 9
HELIX 6 6 ASN A 120 HIS A 124 5 5
HELIX 7 7 GLU A 142 LYS A 155 1 14
HELIX 8 8 ALA A 164 ALA A 168 5 5
HELIX 9 9 HIS A 172 GLY A 177 1 6
HELIX 10 10 GLY A 186 SER A 202 1 17
HELIX 11 11 ILE A 220 LEU A 227 1 8
HELIX 12 12 MET A 239 ASN A 249 1 11
HELIX 13 13 ASP A 258 LYS A 263 1 6
HELIX 14 14 ILE A 264 ASN A 275 1 12
HELIX 15 15 GLY A 316 ALA A 330 1 15
HELIX 16 16 TRP A 344 PHE A 347 5 4
HELIX 17 17 ALA A 348 ARG A 364 1 17
HELIX 18 18 GLY A 372 TRP A 382 1 11
HELIX 19 19 GLY A 394 GLU A 403 1 10
HELIX 20 20 LEU A 407 ALA A 412 1 6
SHEET 1 AA 6 VAL A 92 PHE A 94 0
SHEET 2 AA 6 SER A 114 LEU A 117 1 O VAL A 115 N LEU A 93
SHEET 3 AA 6 SER A 56 MET A 60 1 O VAL A 57 N ILE A 116
SHEET 4 AA 6 ARG A 17 ARG A 21 1 O VAL A 18 N VAL A 58
SHEET 5 AA 6 VAL A 159 ASN A 162 1 O VAL A 159 N VAL A 19
SHEET 6 AA 6 LYS A 183 GLY A 185 1 O ALA A 184 N ASN A 162
SHEET 1 AB 2 MET A 28 LYS A 29 0
SHEET 2 AB 2 GLN A 32 ILE A 33 -1 O GLN A 32 N LYS A 29
SHEET 1 AC 2 LYS A 130 LYS A 132 0
SHEET 2 AC 2 LYS A 138 LYS A 140 -1 O VAL A 139 N GLY A 131
SHEET 1 AD 6 LYS A 278 THR A 280 0
SHEET 2 AD 6 GLU A 232 ILE A 235 1 O MET A 233 N THR A 280
SHEET 3 AD 6 PHE A 207 LEU A 211 1 O ALA A 209 N ILE A 234
SHEET 4 AD 6 GLN A 332 ASN A 336 1 O GLN A 332 N LEU A 208
SHEET 5 AD 6 ILE A 367 ILE A 370 1 O ILE A 367 N ILE A 333
SHEET 6 AD 6 HIS A 390 VAL A 391 1 O HIS A 390 N ILE A 370
SHEET 1 AE 3 THR A 297 THR A 301 0
SHEET 2 AE 3 ASP A 284 ALA A 288 -1 O PHE A 285 N ALA A 300
SHEET 3 AE 3 MET A 311 CYS A 315 -1 O MET A 311 N ALA A 288
CISPEP 1 ARG A 205 PRO A 206 0 5.00
CISPEP 2 ALA A 308 GLY A 309 0 0.17
SITE 1 AC1 11 ASP A 23 ASN A 25 ARG A 38 HIS A 62
SITE 2 AC1 11 ARG A 65 ARG A 122 GLY A 166 THR A 167
SITE 3 AC1 11 ARG A 170 HOH A2024 HOH A2063
SITE 1 AC2 20 GLY A 213 ALA A 214 LYS A 215 LYS A 219
SITE 2 AC2 20 GLY A 237 GLY A 238 LEU A 256 GLY A 312
SITE 3 AC2 20 LEU A 313 ASN A 336 GLY A 337 PRO A 338
SITE 4 AC2 20 GLY A 340 VAL A 341 GLU A 343 GLY A 372
SITE 5 AC2 20 GLY A 373 ASP A 374 THR A 375 HOH A2064
CRYST1 58.620 73.450 93.440 90.00 90.00 90.00 P 21 21 2 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 0.017059 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013615 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010702 0.00000
(ATOM LINES ARE NOT SHOWN.)
END