HEADER TRANSFERASE 27-NOV-09 2WZB
TITLE THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN
TITLE 2 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND MAGNESIUM
TITLE 3 TRIFLUORIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 2-417;
COMPND 5 SYNONYM: PRIMER RECOGNITION PROTEIN 2, PRP 2, CELL MIGRATION-INDUCING
COMPND 6 GENE 10 PROTEIN;
COMPND 7 EC: 2.7.2.3;
COMPND 8 ENGINEERED: YES;
COMPND 9 OTHER_DETAILS: COMPLEXED WITH ADP, 3PG AND MAGNESIUM FLUORIDE
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
KEYWDS HEREDITARY HEMOLYTIC ANEMIA, TRANSFERASE, PHOSPHOPROTEIN, KINASE,
KEYWDS 2 GLYCOLYSIS, NUCLEOTIDE-BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR M.W.BOWLER,M.J.CLIFF,J.P.M.MARSTON,N.J.BAXTER,A.M.H.HOWNSLOW,
AUTHOR 2 A.V.VARGA,J.SZABO,M.VAS,G.M.BLACKBURN,J.P.WALTHO
REVDAT 5 20-DEC-23 2WZB 1 REMARK LINK
REVDAT 4 07-DEC-11 2WZB 1 JRNL
REVDAT 3 13-JUL-11 2WZB 1 VERSN
REVDAT 2 28-APR-10 2WZB 1 JRNL
REVDAT 1 14-APR-10 2WZB 0
JRNL AUTH M.J.CLIFF,M.W.BOWLER,J.SZABO,J.P.M.MARSTON,A.V.VARGA,
JRNL AUTH 2 A.M.H.HOWNSLOW,N.J.BAXTER,G.M.BLACKBURN,M.VAS,J.P.WALTHO
JRNL TITL TRANSITION STATE ANALOGUE STRUCTURES OF HUMAN
JRNL TITL 2 PHOSPHOGLYCERATE KINASE ESTABLISH THE IMPORTANCE OF CHARGE
JRNL TITL 3 BALANCE IN CATALYSIS.
JRNL REF J.AM.CHEM.SOC. V. 132 6507 2010
JRNL REFN ISSN 0002-7863
JRNL PMID 20397725
JRNL DOI 10.1021/JA100974T
REMARK 2
REMARK 2 RESOLUTION. 1.47 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0070
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) : 1.47
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 64731
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) : 0.162
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3452
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) : 1.47
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.50
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4535
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.62
REMARK 3 BIN R VALUE (WORKING SET) : 0.2330
REMARK 3 BIN FREE R VALUE SET COUNT : 229
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3040
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 44
REMARK 3 SOLVENT ATOMS : 617
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 13.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.78
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.64000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : -0.65000
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): 0.066
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.088
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3143 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2133 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4245 ; 1.779 ; 1.994
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5265 ; 0.936 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 9.022 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;42.078 ;25.678
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 570 ;12.335 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;16.678 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 485 ; 0.084 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3450 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 564 ; 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): 2007 ; 0.655 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 833 ; 0.198 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3215 ; 1.121 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 1.980 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1028 ; 3.093 ; 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 : 2
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 1 A 189
REMARK 3 ORIGIN FOR THE GROUP (A): 3.4831 3.5463 -5.3699
REMARK 3 T TENSOR
REMARK 3 T11: 0.1262 T22: 0.0616
REMARK 3 T33: 0.0071 T12: 0.0588
REMARK 3 T13: -0.0062 T23: -0.0146
REMARK 3 L TENSOR
REMARK 3 L11: 1.7697 L22: 3.3143
REMARK 3 L33: 2.6601 L12: -1.0454
REMARK 3 L13: 0.6540 L23: -0.8658
REMARK 3 S TENSOR
REMARK 3 S11: -0.2395 S12: -0.2508 S13: 0.0888
REMARK 3 S21: 0.6075 S22: 0.2477 S23: -0.0164
REMARK 3 S31: -0.3114 S32: -0.1767 S33: -0.0081
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 190 A 416
REMARK 3 ORIGIN FOR THE GROUP (A): -5.7377 10.5787 -32.0892
REMARK 3 T TENSOR
REMARK 3 T11: 0.0163 T22: 0.0425
REMARK 3 T33: 0.0269 T12: -0.0064
REMARK 3 T13: -0.0019 T23: -0.0108
REMARK 3 L TENSOR
REMARK 3 L11: 1.1237 L22: 1.6006
REMARK 3 L33: 0.9881 L12: -0.5265
REMARK 3 L13: 0.1417 L23: -0.4487
REMARK 3 S TENSOR
REMARK 3 S11: 0.0401 S12: 0.0615 S13: -0.0110
REMARK 3 S21: -0.1217 S22: -0.0308 S23: 0.0602
REMARK 3 S31: 0.0231 S32: -0.0143 S33: -0.0093
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 2WZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-09.
REMARK 100 THE DEPOSITION ID IS D_1290041848.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-JAN-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
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 : C111
REMARK 200 OPTICS : GE211
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 : 68247
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470
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 : 3.600
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.50
REMARK 200 R MERGE FOR SHELL (I) : 0.32000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300
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: PDB ENTRY 3C39
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG2000MME, 0.1M BIS/TRIS PH 6.5
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 19.71500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.50000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.09000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.50000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.71500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.09000
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 SER A 1
REMARK 465 LYS A 132
REMARK 465 ASP A 133
REMARK 465 ALA A 134
REMARK 465 SER A 135
REMARK 465 GLY A 136
REMARK 465 ASN A 137
REMARK 465 LYS A 138
REMARK 465 VAL A 139
REMARK 465 LYS A 140
REMARK 465 ALA A 141
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 OE2 GLU A 128 O HOH A 2263 2.18
REMARK 500 NZ LYS A 290 O HOH A 2465 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 GLU A 128 CA GLU A 128 C -0.208
REMARK 500 GLU A 128 CA GLU A 128 C -0.203
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 120 116.28 -35.40
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2082 DISTANCE = 6.64 ANGSTROMS
REMARK 525 HOH A2087 DISTANCE = 6.06 ANGSTROMS
REMARK 525 HOH A2088 DISTANCE = 6.04 ANGSTROMS
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 MG A1417 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 374 OD2
REMARK 620 2 ADP A1419 O1B 88.2
REMARK 620 3 ADP A1419 O1A 95.9 91.4
REMARK 620 4 MGF A1421 F1 175.2 87.8 86.8
REMARK 620 5 HOH A2608 O 89.3 177.5 88.9 94.7
REMARK 620 6 HOH A2614 O 94.1 92.9 169.2 83.5 87.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MGF A1421 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A1419 O3B
REMARK 620 2 MGF A1421 F1 92.0
REMARK 620 3 MGF A1421 F2 94.5 122.9
REMARK 620 4 MGF A1421 F3 86.8 117.0 119.9
REMARK 620 5 3PG A1420 O2 170.9 94.8 86.8 84.8
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1417
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1418
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1419
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 1420
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MGF A 1421
REMARK 900
REMARK 900 RELATED ENTRIES
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: 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
DBREF 2WZB A 1 416 UNP P00558 PGK1_HUMAN 2 417
SEQRES 1 A 416 SER LEU SER ASN LYS LEU THR LEU ASP LYS LEU ASP VAL
SEQRES 2 A 416 LYS GLY LYS ARG VAL VAL MET ARG VAL ASP PHE ASN VAL
SEQRES 3 A 416 PRO MET LYS ASN ASN GLN ILE THR ASN ASN GLN ARG ILE
SEQRES 4 A 416 LYS ALA ALA VAL PRO SER ILE LYS PHE CYS LEU ASP ASN
SEQRES 5 A 416 GLY ALA LYS SER VAL VAL LEU MET SER HIS LEU GLY ARG
SEQRES 6 A 416 PRO ASP GLY VAL PRO MET PRO ASP LYS TYR SER LEU GLU
SEQRES 7 A 416 PRO VAL ALA VAL GLU LEU LYS SER LEU LEU GLY LYS ASP
SEQRES 8 A 416 VAL LEU PHE LEU LYS ASP CYS VAL GLY PRO GLU VAL GLU
SEQRES 9 A 416 LYS ALA CYS ALA ASN PRO ALA ALA GLY SER VAL ILE LEU
SEQRES 10 A 416 LEU GLU ASN LEU ARG PHE HIS VAL GLU GLU GLU GLY LYS
SEQRES 11 A 416 GLY LYS ASP ALA SER GLY ASN LYS VAL LYS ALA GLU PRO
SEQRES 12 A 416 ALA LYS ILE GLU ALA PHE ARG ALA SER LEU SER LYS LEU
SEQRES 13 A 416 GLY ASP VAL TYR VAL ASN ASP ALA PHE GLY THR ALA HIS
SEQRES 14 A 416 ARG ALA HIS SER SER MET VAL GLY VAL ASN LEU PRO GLN
SEQRES 15 A 416 LYS ALA GLY GLY PHE LEU MET LYS LYS GLU LEU ASN TYR
SEQRES 16 A 416 PHE ALA LYS ALA LEU GLU SER PRO GLU ARG PRO PHE LEU
SEQRES 17 A 416 ALA ILE LEU GLY GLY ALA LYS VAL ALA ASP LYS ILE GLN
SEQRES 18 A 416 LEU ILE ASN ASN MET LEU ASP LYS VAL ASN GLU MET ILE
SEQRES 19 A 416 ILE GLY GLY GLY MET ALA PHE THR PHE LEU LYS VAL LEU
SEQRES 20 A 416 ASN ASN MET GLU ILE GLY THR SER LEU PHE ASP GLU GLU
SEQRES 21 A 416 GLY ALA LYS ILE VAL LYS ASP LEU MET SER LYS ALA GLU
SEQRES 22 A 416 LYS ASN GLY VAL LYS ILE THR LEU PRO VAL ASP PHE VAL
SEQRES 23 A 416 THR ALA ASP LYS PHE ASP GLU ASN ALA LYS THR GLY GLN
SEQRES 24 A 416 ALA THR VAL ALA SER GLY ILE PRO ALA GLY TRP MET GLY
SEQRES 25 A 416 LEU ASP CYS GLY PRO GLU SER SER LYS LYS TYR ALA GLU
SEQRES 26 A 416 ALA VAL THR ARG ALA LYS GLN ILE VAL TRP ASN GLY PRO
SEQRES 27 A 416 VAL GLY VAL PHE GLU TRP GLU ALA PHE ALA ARG GLY THR
SEQRES 28 A 416 LYS ALA LEU MET ASP GLU VAL VAL LYS ALA THR SER ARG
SEQRES 29 A 416 GLY CYS ILE THR ILE ILE GLY GLY GLY ASP THR ALA THR
SEQRES 30 A 416 CYS CYS ALA LYS TRP ASN THR GLU ASP LYS VAL SER HIS
SEQRES 31 A 416 VAL SER THR GLY GLY GLY ALA SER LEU GLU LEU LEU GLU
SEQRES 32 A 416 GLY LYS VAL LEU PRO GLY VAL ASP ALA LEU SER ASN ILE
HET MG A1417 1
HET CL A1418 1
HET ADP A1419 27
HET 3PG A1420 11
HET MGF A1421 4
HETNAM MG MAGNESIUM ION
HETNAM CL CHLORIDE ION
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM 3PG 3-PHOSPHOGLYCERIC ACID
HETNAM MGF TRIFLUOROMAGNESATE
FORMUL 2 MG MG 2+
FORMUL 3 CL CL 1-
FORMUL 4 ADP C10 H15 N5 O10 P2
FORMUL 5 3PG C3 H7 O7 P
FORMUL 6 MGF F3 MG 1-
FORMUL 7 HOH *617(H2 O)
HELIX 1 1 LEU A 8 LEU A 11 5 4
HELIX 2 2 ASN A 36 ASN A 52 1 17
HELIX 3 3 MET A 71 SER A 76 1 6
HELIX 4 4 LEU A 77 GLY A 89 1 13
HELIX 5 5 GLY A 100 ASN A 109 1 10
HELIX 6 6 ASN A 120 HIS A 124 5 5
HELIX 7 7 GLU A 142 LEU A 156 1 15
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 LYS A 215 ILE A 220 1 6
HELIX 12 12 LEU A 222 LEU A 227 1 6
HELIX 13 13 MET A 239 ASN A 249 1 11
HELIX 14 14 ASP A 258 LYS A 263 1 6
HELIX 15 15 ILE A 264 ASN A 275 1 12
HELIX 16 16 GLY A 316 ALA A 330 1 15
HELIX 17 17 TRP A 344 PHE A 347 5 4
HELIX 18 18 ALA A 348 ARG A 364 1 17
HELIX 19 19 ASP A 374 TRP A 382 1 9
HELIX 20 20 GLY A 395 GLY A 404 1 10
HELIX 21 21 LEU A 407 ALA A 412 1 6
SHEET 1 AA 6 LEU A 93 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 6 LYS A 278 THR A 280 0
SHEET 2 AC 6 GLU A 232 ILE A 235 1 O MET A 233 N THR A 280
SHEET 3 AC 6 PHE A 207 LEU A 211 1 O ALA A 209 N ILE A 234
SHEET 4 AC 6 GLN A 332 ASN A 336 1 O GLN A 332 N LEU A 208
SHEET 5 AC 6 ILE A 367 GLY A 371 1 O ILE A 367 N ILE A 333
SHEET 6 AC 6 HIS A 390 SER A 392 1 O HIS A 390 N ILE A 370
SHEET 1 AD 3 THR A 297 THR A 301 0
SHEET 2 AD 3 ASP A 284 ALA A 288 -1 O PHE A 285 N ALA A 300
SHEET 3 AD 3 MET A 311 CYS A 315 -1 O MET A 311 N ALA A 288
LINK OD2 ASP A 374 MG MG A1417 1555 1555 2.11
LINK MG MG A1417 O1B ADP A1419 1555 1555 2.07
LINK MG MG A1417 O1A ADP A1419 1555 1555 2.06
LINK MG MG A1417 F1 MGF A1421 1555 1555 1.97
LINK MG MG A1417 O HOH A2608 1555 1555 2.15
LINK MG MG A1417 O HOH A2614 1555 1555 2.13
LINK O3B ADP A1419 MG MGF A1421 1555 1555 2.15
LINK O2 3PG A1420 MG MGF A1421 1555 1555 2.13
CISPEP 1 ARG A 205 PRO A 206 0 3.58
SITE 1 AC1 5 ASP A 374 ADP A1419 MGF A1421 HOH A2608
SITE 2 AC1 5 HOH A2614
SITE 1 AC2 4 ARG A 65 LYS A 215 ASP A 218 HOH A2362
SITE 1 AC3 29 GLY A 213 ALA A 214 LYS A 215 LYS A 219
SITE 2 AC3 29 GLY A 237 GLY A 238 LEU A 256 GLY A 312
SITE 3 AC3 29 ASN A 336 PRO A 338 GLY A 340 VAL A 341
SITE 4 AC3 29 GLU A 343 GLY A 371 GLY A 372 GLY A 373
SITE 5 AC3 29 ASP A 374 THR A 375 MG A1417 MGF A1421
SITE 6 AC3 29 HOH A2527 HOH A2557 HOH A2608 HOH A2609
SITE 7 AC3 29 HOH A2610 HOH A2611 HOH A2612 HOH A2613
SITE 8 AC3 29 HOH A2614
SITE 1 AC4 15 ASP A 23 ASN A 25 ARG A 38 HIS A 62
SITE 2 AC4 15 ARG A 65 ARG A 122 GLY A 166 ARG A 170
SITE 3 AC4 15 LYS A 215 MGF A1421 HOH A2303 HOH A2614
SITE 4 AC4 15 HOH A2615 HOH A2616 HOH A2617
SITE 1 AC5 13 ARG A 38 LYS A 215 LYS A 219 GLY A 372
SITE 2 AC5 13 GLY A 373 GLY A 395 GLY A 396 MG A1417
SITE 3 AC5 13 ADP A1419 3PG A1420 HOH A2608 HOH A2614
SITE 4 AC5 13 HOH A2617
CRYST1 39.430 92.180 109.000 90.00 90.00 90.00 P 21 21 21 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 0.025361 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010848 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009174 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
