PDB Short entry for 2YBE HEADER TRANSFERASE 07-MAR-11 2YBE TITLE THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN COMPLEX TITLE 2 WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE AT 2.0 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOGLYCERATE KINASE, CELL MIGRATION-INDUCING GENE 10 COMPND 5 PROTEIN, PRIMER RECOGNITION PROTEIN 2, PRP 2; 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 KEYWDS TRANSFERASE, L-NUCLEOSIDE ANALOGUES, GLYCOLYSIS, NUCLEOTIDE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.W.BOWLER,L.CHALOIN,C.LIONNE REVDAT 3 20-DEC-23 2YBE 1 REMARK LINK REVDAT 2 29-JUN-11 2YBE 1 COMPND KEYWDS JRNL REMARK REVDAT 1 27-APR-11 2YBE 0 JRNL AUTH P.LALLEMAND,L.CHALOIN,B.ROY,T.BARMAN,M.W.BOWLER,C.LIONNE JRNL TITL INTERACTION OF HUMAN 3-PHOSPHOGLYCERATE KINASE WITH ITS TWO JRNL TITL 2 SUBSTRATES: IS SUBSTRATE ANTAGONISM A KINETIC ADVANTAGE? JRNL REF J.MOL.BIOL. V. 409 742 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21549713 JRNL DOI 10.1016/J.JMB.2011.04.048 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0107 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 24020 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1287 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1419 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.4360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61000 REMARK 3 B22 (A**2) : 3.08000 REMARK 3 B33 (A**2) : -2.46000 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): 0.218 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.172 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.603 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3171 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2155 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4280 ; 1.866 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5307 ; 1.039 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 408 ; 7.387 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;42.522 ;25.641 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 578 ;17.816 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.623 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3465 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 561 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 2 A 416 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4060 -7.2070 -19.4120 REMARK 3 T TENSOR REMARK 3 T11: 1.0909 T22: 0.9225 REMARK 3 T33: 0.0280 T12: -0.2032 REMARK 3 T13: -0.0527 T23: -0.1268 REMARK 3 L TENSOR REMARK 3 L11: 2.0711 L22: 1.7213 REMARK 3 L33: 4.8596 L12: 0.4660 REMARK 3 L13: -0.7515 L23: -0.8805 REMARK 3 S TENSOR REMARK 3 S11: -0.2872 S12: 1.2534 S13: -0.1460 REMARK 3 S21: -1.3017 S22: 0.3470 S23: 0.0395 REMARK 3 S31: 0.7461 S32: -0.5992 S33: -0.0597 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 2YBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-11 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 : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.932 REMARK 200 MONOCHROMATOR : DIAMOND 001 REMARK 200 OPTICS : GE 221 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25350 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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 2WZC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG 2000MME, 0.1 M BIS/TRIS PH REMARK 280 6.25 ., 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 19.60100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.40350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.51500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.40350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.60100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.51500 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 ASP A 133 REMARK 465 ALA A 134 REMARK 465 SER A 135 REMARK 465 GLY A 136 REMARK 465 ASN A 137 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 C LYS A 132 O HOH A 2040 1.66 REMARK 500 NZ LYS A 10 O HOH A 2003 2.10 REMARK 500 ND1 HIS A 390 O HOH A 2098 2.15 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 NZ LYS A 105 OE2 GLU A 201 2554 1.74 REMARK 500 O ALA A 112 NZ LYS A 321 2454 2.17 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 72.54 -154.25 REMARK 500 ASN A 120 111.65 -31.56 REMARK 500 ASN A 249 38.88 39.23 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 GLU A 128 GLY A 129 -46.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ADENOSINE-5'-DIPHOSPHATE (ADP): THIS IS THE L-ENANTIOMER OF REMARK 600 ADP 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 LA8 A1419 O3B 98.6 REMARK 620 3 LA8 A1419 O1A 99.6 97.2 REMARK 620 4 HOH A2112 O 87.1 173.1 77.9 REMARK 620 5 HOH A2115 O 93.7 99.8 156.6 83.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ALF A1420 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LA8 A1419 O1B REMARK 620 2 ALF A1420 F1 84.0 REMARK 620 3 ALF A1420 F2 86.3 89.0 REMARK 620 4 ALF A1420 F3 93.0 90.5 179.2 REMARK 620 5 ALF A1420 F4 96.6 179.1 91.6 88.8 REMARK 620 6 3PG A1421 O2 175.4 91.5 94.1 86.5 87.9 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 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 LA8 A 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALF A 1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 1421 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XE7 RELATED DB: PDB REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE REMARK 900 OPEN TERNARY COMPLEX WITH 3PG AND ADP REMARK 900 RELATED ID: 2Y3I RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN REMARK 900 COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM 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: 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: 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: 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: 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: 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 2YBE 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 MG A1417 1 HET CL A1418 1 HET LA8 A1419 27 HET ALF A1420 5 HET 3PG A1421 11 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM LA8 L-ADENOSINE-5'-DIPHOSPHATE HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM 3PG 3-PHOSPHOGLYCERIC ACID HETSYN LA8 L-ADP FORMUL 2 MG MG 2+ FORMUL 3 CL CL 1- FORMUL 4 LA8 C10 H15 N5 O10 P2 FORMUL 5 ALF AL F4 1- FORMUL 6 3PG C3 H7 O7 P FORMUL 7 HOH *116(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 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 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 ASN A 275 1 18 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 ASP A 374 TRP A 382 1 9 HELIX 19 19 GLY A 395 GLY A 404 1 10 HELIX 20 20 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 2 LYS A 130 GLY A 131 0 SHEET 2 AC 2 VAL A 139 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 GLY A 371 1 O ILE A 367 N ILE A 333 SHEET 6 AD 6 HIS A 390 SER A 392 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 LINK OD2 ASP A 374 MG MG A1417 1555 1555 2.00 LINK MG MG A1417 O3B LA8 A1419 1555 1555 1.82 LINK MG MG A1417 O1A LA8 A1419 1555 1555 1.87 LINK MG MG A1417 O HOH A2112 1555 1555 2.01 LINK MG MG A1417 O HOH A2115 1555 1555 2.23 LINK O1B LA8 A1419 AL ALF A1420 1555 1555 1.95 LINK AL ALF A1420 O2 3PG A1421 1555 1555 1.95 CISPEP 1 ARG A 205 PRO A 206 0 -3.20 SITE 1 AC1 5 ASP A 374 LA8 A1419 ALF A1420 HOH A2112 SITE 2 AC1 5 HOH A2115 SITE 1 AC2 4 ARG A 65 LYS A 215 ALA A 217 ASP A 218 SITE 1 AC3 22 GLY A 213 ALA A 214 LYS A 215 LYS A 219 SITE 2 AC3 22 GLY A 238 ASN A 336 PRO A 338 GLY A 340 SITE 3 AC3 22 VAL A 341 PHE A 342 GLU A 343 GLY A 371 SITE 4 AC3 22 GLY A 372 GLY A 373 ASP A 374 THR A 375 SITE 5 AC3 22 MG A1417 ALF A1420 HOH A2110 HOH A2111 SITE 6 AC3 22 HOH A2112 HOH A2113 SITE 1 AC4 14 ARG A 38 LYS A 215 LYS A 219 GLY A 372 SITE 2 AC4 14 GLY A 373 GLY A 395 GLY A 396 MG A1417 SITE 3 AC4 14 LA8 A1419 3PG A1421 HOH A2047 HOH A2112 SITE 4 AC4 14 HOH A2114 HOH A2115 SITE 1 AC5 14 ASP A 23 ASN A 25 ARG A 38 HIS A 62 SITE 2 AC5 14 ARG A 65 ARG A 122 GLY A 166 THR A 167 SITE 3 AC5 14 ARG A 170 LYS A 215 ALF A1420 HOH A2114 SITE 4 AC5 14 HOH A2115 HOH A2116 CRYST1 39.202 91.030 108.807 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 0.025509 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009191 0.00000