PDB Short entry for 2X14 HEADER TRANSFERASE 21-DEC-09 2X14 TITLE THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN TITLE 2 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH AMP-PCP AND 3PG 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; COMPND 8 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: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TRANSITION STATE ANALOGUE, HEREDITARY HEMOLYTIC ANEMIA, ATP-BINDING, KEYWDS 2 KINASE, GLYCOLYSIS, TRANSFERASE, DISEASE MUTATION 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 2 20-DEC-23 2X14 1 REMARK LINK REVDAT 1 29-DEC-10 2X14 0 JRNL AUTH M.W.BOWLER,M.J.CLIFF,J.P.M.MARSTON,N.J.BAXTER, JRNL AUTH 2 A.M.H.HOWNSLOW,A.V.VARGA,J.SZABO,M.VAS,G.M.BLACKBURN, JRNL AUTH 3 J.P.WALTHO JRNL TITL THE STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE IN ITS FULLY JRNL TITL 2 ACTIVE CONFORMATION IN COMPLEX WITH GROUND STATE ANALOGUES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 25803 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1388 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1367 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3036 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 1.64000 REMARK 3 B33 (A**2) : -2.13000 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): 0.195 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.378 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3128 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2114 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4227 ; 1.468 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5201 ; 0.889 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 6.620 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;43.164 ;25.641 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 561 ;13.511 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3430 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 556 ; 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): 2002 ; 0.604 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 830 ; 0.178 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3204 ; 1.033 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1126 ; 1.811 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1023 ; 2.803 ; 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): 3.3769 3.5257 -5.3122 REMARK 3 T TENSOR REMARK 3 T11: 0.1169 T22: 0.0611 REMARK 3 T33: 0.0077 T12: 0.0453 REMARK 3 T13: 0.0027 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.9215 L22: 3.7817 REMARK 3 L33: 2.8509 L12: -0.8471 REMARK 3 L13: 0.8770 L23: -0.8378 REMARK 3 S TENSOR REMARK 3 S11: -0.2035 S12: -0.2731 S13: 0.0933 REMARK 3 S21: 0.6376 S22: 0.2073 S23: 0.0218 REMARK 3 S31: -0.2967 S32: -0.2070 S33: -0.0038 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): -5.6521 10.2989 -31.7665 REMARK 3 T TENSOR REMARK 3 T11: 0.0113 T22: 0.0417 REMARK 3 T33: 0.0409 T12: -0.0049 REMARK 3 T13: -0.0031 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.0035 L22: 1.3752 REMARK 3 L33: 1.2138 L12: -0.4575 REMARK 3 L13: 0.2995 L23: -0.5290 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: 0.0207 S13: 0.0137 REMARK 3 S21: -0.0996 S22: -0.0075 S23: 0.1022 REMARK 3 S31: -0.0030 S32: -0.0481 S33: -0.0051 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 2X14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1290042167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-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 : DIAMOND 111 REMARK 200 OPTICS : GE 211 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 : 27244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 86.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 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 2WZB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS/TRIS PH 6.5, 21% P2000MME 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 19.67000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.24000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.24000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.81500 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 220 TO ALA 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 2 REMARK 465 LYS A 133 REMARK 465 ASP A 134 REMARK 465 ALA A 135 REMARK 465 SER A 136 REMARK 465 GLY A 137 REMARK 465 ASN A 138 REMARK 465 LYS A 139 REMARK 465 VAL A 140 REMARK 465 LYS A 141 REMARK 465 ALA A 142 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 31 -118.37 47.14 REMARK 500 ASN A 110 67.12 -155.25 REMARK 500 ASN A 121 112.36 -36.12 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 MG A1418 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 375 OD2 REMARK 620 2 ACP A1420 O2B 92.3 REMARK 620 3 ACP A1420 O1A 93.7 95.2 REMARK 620 4 ACP A1420 O1G 178.1 88.4 84.5 REMARK 620 5 HOH A2208 O 98.1 91.5 166.2 83.6 REMARK 620 6 HOH A2217 O 89.9 177.4 83.3 89.4 89.6 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 1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP A 1420 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: 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: 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 2X14 A 2 417 UNP P00558 PGK1_HUMAN 2 417 SEQADV 2X14 ALA A 220 UNP P00558 LYS 220 ENGINEERED MUTATION 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 ALA 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 A1418 1 HET 3PG A1419 11 HET ACP A1420 31 HETNAM MG MAGNESIUM ION HETNAM 3PG 3-PHOSPHOGLYCERIC ACID HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 3PG C3 H7 O7 P FORMUL 4 ACP C11 H18 N5 O12 P3 FORMUL 5 HOH *218(H2 O) HELIX 1 1 LEU A 9 LEU A 12 5 4 HELIX 2 2 ASN A 37 ALA A 42 1 6 HELIX 3 3 ALA A 43 ASN A 53 1 11 HELIX 4 4 MET A 72 SER A 77 1 6 HELIX 5 5 LEU A 78 GLY A 90 1 13 HELIX 6 6 GLY A 101 ASN A 110 1 10 HELIX 7 7 ASN A 121 HIS A 125 5 5 HELIX 8 8 GLU A 143 LYS A 156 1 14 HELIX 9 9 ALA A 165 ALA A 169 5 5 HELIX 10 10 HIS A 173 GLY A 178 1 6 HELIX 11 11 GLY A 187 LEU A 201 1 15 HELIX 12 12 LYS A 216 GLN A 222 1 7 HELIX 13 13 LEU A 223 LEU A 228 1 6 HELIX 14 14 MET A 240 ASN A 250 1 11 HELIX 15 15 ASP A 259 LYS A 264 1 6 HELIX 16 16 ILE A 265 GLY A 277 1 13 HELIX 17 17 GLY A 317 ALA A 331 1 15 HELIX 18 18 TRP A 345 PHE A 348 5 4 HELIX 19 19 ALA A 349 ARG A 365 1 17 HELIX 20 20 ASP A 375 ASN A 384 1 10 HELIX 21 21 GLY A 396 GLU A 404 1 9 HELIX 22 22 LEU A 408 ALA A 413 1 6 SHEET 1 AA 6 LEU A 94 PHE A 95 0 SHEET 2 AA 6 SER A 115 LEU A 118 1 O VAL A 116 N LEU A 94 SHEET 3 AA 6 SER A 57 MET A 61 1 O VAL A 58 N ILE A 117 SHEET 4 AA 6 ARG A 18 ARG A 22 1 O VAL A 19 N VAL A 59 SHEET 5 AA 6 VAL A 160 ASN A 163 1 O VAL A 160 N VAL A 20 SHEET 6 AA 6 LYS A 184 GLY A 186 1 O ALA A 185 N ASN A 163 SHEET 1 AB 2 MET A 29 LYS A 30 0 SHEET 2 AB 2 GLN A 33 ILE A 34 -1 O GLN A 33 N LYS A 30 SHEET 1 AC 6 LYS A 279 THR A 281 0 SHEET 2 AC 6 GLU A 233 ILE A 236 1 O MET A 234 N THR A 281 SHEET 3 AC 6 PHE A 208 LEU A 212 1 O ALA A 210 N ILE A 235 SHEET 4 AC 6 GLN A 333 ASN A 337 1 O GLN A 333 N LEU A 209 SHEET 5 AC 6 ILE A 368 GLY A 372 1 O ILE A 368 N ILE A 334 SHEET 6 AC 6 HIS A 391 VAL A 392 1 O HIS A 391 N ILE A 371 SHEET 1 AD 3 THR A 298 THR A 302 0 SHEET 2 AD 3 ASP A 285 ALA A 289 -1 O PHE A 286 N ALA A 301 SHEET 3 AD 3 MET A 312 CYS A 316 -1 O MET A 312 N ALA A 289 LINK OD2 ASP A 375 MG MG A1418 1555 1555 2.08 LINK MG MG A1418 O2B ACP A1420 1555 1555 1.91 LINK MG MG A1418 O1A ACP A1420 1555 1555 1.99 LINK MG MG A1418 O1G ACP A1420 1555 1555 2.17 LINK MG MG A1418 O HOH A2208 1555 1555 2.11 LINK MG MG A1418 O HOH A2217 1555 1555 2.02 CISPEP 1 VAL A 100 GLY A 101 0 -23.65 CISPEP 2 GLU A 129 GLY A 130 0 -28.97 CISPEP 3 ARG A 206 PRO A 207 0 1.48 SITE 1 AC1 4 ASP A 375 ACP A1420 HOH A2208 HOH A2217 SITE 1 AC2 16 ASP A 24 ASN A 26 ARG A 39 HIS A 63 SITE 2 AC2 16 ARG A 66 ARG A 123 GLY A 167 THR A 168 SITE 3 AC2 16 ARG A 171 LYS A 216 ACP A1420 HOH A2069 SITE 4 AC2 16 HOH A2207 HOH A2208 HOH A2209 HOH A2211 SITE 1 AC3 34 ARG A 39 GLY A 214 ALA A 215 LYS A 216 SITE 2 AC3 34 GLY A 238 GLY A 239 LEU A 257 GLY A 313 SITE 3 AC3 34 LEU A 314 ASN A 337 PRO A 339 GLY A 341 SITE 4 AC3 34 VAL A 342 GLU A 344 GLY A 372 GLY A 373 SITE 5 AC3 34 GLY A 374 ASP A 375 THR A 376 GLY A 396 SITE 6 AC3 34 GLY A 397 MG A1418 3PG A1419 HOH A2175 SITE 7 AC3 34 HOH A2208 HOH A2210 HOH A2211 HOH A2212 SITE 8 AC3 34 HOH A2213 HOH A2214 HOH A2215 HOH A2216 SITE 9 AC3 34 HOH A2217 HOH A2218 CRYST1 39.340 91.630 108.480 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 0.025419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009218 0.00000