HEADER TRANSFERASE 10-OCT-16 5M1R TITLE X-RAY STRUCTURE OF HUMAN G166D PGK-1 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL MIGRATION-INDUCING GENE 10 PROTEIN,PRIMER RECOGNITION COMPND 5 PROTEIN 2,PRP 2; COMPND 6 EC: 2.7.2.3; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: G166D PGK-1 MUTANT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PGK1, PGKA, MIG10, OK/SW-CL.110; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOGLYCERATE KINASE, SINGLE NUCLEOTIDE POLYMORPHISM DERIVED KEYWDS 2 MUTANT G166D, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ILARI,A.CIPOLLONE,A.FIORILLO,M.PETROSINO REVDAT 3 17-JAN-24 5M1R 1 LINK REVDAT 2 12-DEC-18 5M1R 1 JRNL REVDAT 1 20-DEC-17 5M1R 0 JRNL AUTH A.FIORILLO,M.PETROSINO,A.ILARI,A.PASQUO,A.CIPOLLONE,M.MAGGI, JRNL AUTH 2 R.CHIARALUCE,V.CONSALVI JRNL TITL THE PHOSPHOGLYCERATE KINASE 1 VARIANTS FOUND IN CARCINOMA JRNL TITL 2 CELLS DISPLAY DIFFERENT CATALYTIC ACTIVITY AND JRNL TITL 3 CONFORMATIONAL STABILITY COMPARED TO THE NATIVE ENZYME. JRNL REF PLOS ONE V. 13 99191 2018 JRNL REFN ESSN 1932-6203 JRNL PMID 29995887 JRNL DOI 10.1371/JOURNAL.PONE.0199191 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 42334 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2196 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3120 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3270 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3214 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4430 ; 1.667 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7448 ; 0.968 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 8.949 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;43.489 ;25.887 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 597 ;15.058 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.423 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3662 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 661 ; 0.002 ; 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): 1677 ; 1.479 ; 1.905 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1676 ; 1.469 ; 1.903 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2098 ; 2.351 ; 2.853 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2099 ; 2.351 ; 2.854 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1593 ; 2.275 ; 2.231 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1594 ; 2.274 ; 2.231 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2326 ; 3.674 ; 3.208 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3597 ; 5.531 ;23.682 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3551 ; 5.479 ;23.380 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5M1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-16 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.820 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: 2ZGV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, 1.6 M, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 52.78500 REMARK 290 SMTRY3 2 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 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 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 OE1 GLU A 147 O HOH A 601 2.00 REMARK 500 OE2 GLU A 142 O HOH A 602 2.16 REMARK 500 O1A ADP A 501 O HOH A 603 2.19 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 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.1 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 31 -6.25 68.17 REMARK 500 ASN A 109 67.18 -160.78 REMARK 500 ASN A 120 115.24 -37.01 REMARK 500 ALA A 164 68.08 -118.70 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 ARG A 205 PRO A 206 43.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 205 12.97 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 A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 372 O REMARK 620 2 THR A 375 OG1 130.6 REMARK 620 3 ADP A 501 O1B 129.0 80.8 REMARK 620 4 HOH A 608 O 83.5 87.5 144.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 605 O REMARK 620 2 HOH A 810 O 126.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 DBREF 5M1R A 1 416 UNP P00558 PGK1_HUMAN 2 417 SEQADV 5M1R ASP A 166 UNP P00558 GLY 167 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 ASP 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 ADP A 501 54 HET MG A 502 1 HET MG A 503 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *239(H2 O) HELIX 1 AA1 SER A 1 LYS A 5 5 5 HELIX 2 AA2 THR A 7 LEU A 11 5 5 HELIX 3 AA3 ASN A 36 ASN A 52 1 17 HELIX 4 AA4 MET A 71 SER A 76 1 6 HELIX 5 AA5 LEU A 77 GLY A 89 1 13 HELIX 6 AA6 GLY A 100 ASN A 109 1 10 HELIX 7 AA7 ASN A 120 HIS A 124 5 5 HELIX 8 AA8 GLU A 142 LYS A 155 1 14 HELIX 9 AA9 ALA A 164 ALA A 168 5 5 HELIX 10 AB1 HIS A 172 GLY A 177 1 6 HELIX 11 AB2 GLY A 186 GLU A 201 1 16 HELIX 12 AB3 VAL A 216 ASP A 218 5 3 HELIX 13 AB4 LYS A 219 ASP A 228 1 10 HELIX 14 AB5 GLY A 238 ASN A 249 1 12 HELIX 15 AB6 ASP A 258 LYS A 263 1 6 HELIX 16 AB7 ILE A 264 GLY A 276 1 13 HELIX 17 AB8 GLY A 316 ALA A 330 1 15 HELIX 18 AB9 TRP A 344 PHE A 347 5 4 HELIX 19 AC1 ALA A 348 ARG A 364 1 17 HELIX 20 AC2 GLY A 373 TRP A 382 1 10 HELIX 21 AC3 GLY A 394 GLU A 403 1 10 HELIX 22 AC4 LEU A 407 ALA A 412 1 6 SHEET 1 AA1 6 LEU A 93 PHE A 94 0 SHEET 2 AA1 6 SER A 114 LEU A 117 1 O VAL A 115 N LEU A 93 SHEET 3 AA1 6 SER A 56 MET A 60 1 N LEU A 59 O ILE A 116 SHEET 4 AA1 6 ARG A 17 VAL A 22 1 N MET A 20 O VAL A 58 SHEET 5 AA1 6 VAL A 159 ASP A 163 1 O ASP A 163 N ARG A 21 SHEET 6 AA1 6 LYS A 183 GLY A 185 1 O ALA A 184 N TYR A 160 SHEET 1 AA2 2 MET A 28 LYS A 29 0 SHEET 2 AA2 2 GLN A 32 ILE A 33 -1 O GLN A 32 N LYS A 29 SHEET 1 AA3 2 LYS A 130 LYS A 132 0 SHEET 2 AA3 2 LYS A 138 LYS A 140 -1 O VAL A 139 N GLY A 131 SHEET 1 AA4 6 LYS A 278 THR A 280 0 SHEET 2 AA4 6 GLU A 232 ILE A 235 1 N MET A 233 O THR A 280 SHEET 3 AA4 6 PHE A 207 LEU A 211 1 N LEU A 211 O ILE A 234 SHEET 4 AA4 6 GLN A 332 ASN A 336 1 O ASN A 336 N ILE A 210 SHEET 5 AA4 6 ILE A 367 ILE A 370 1 O ILE A 369 N ILE A 333 SHEET 6 AA4 6 HIS A 390 VAL A 391 1 O HIS A 390 N ILE A 370 SHEET 1 AA5 3 THR A 297 THR A 301 0 SHEET 2 AA5 3 ASP A 284 ALA A 288 -1 N PHE A 285 O ALA A 300 SHEET 3 AA5 3 MET A 311 CYS A 315 -1 O MET A 311 N ALA A 288 LINK O GLY A 372 MG MG A 502 1555 1555 2.52 LINK OG1 THR A 375 MG MG A 502 1555 1555 2.68 LINK O1BAADP A 501 MG MG A 502 1555 1555 1.99 LINK MG MG A 502 O HOH A 608 1555 1555 1.92 LINK MG MG A 503 O HOH A 605 1555 1555 2.06 LINK MG MG A 503 O HOH A 810 1555 1555 2.50 SITE 1 AC1 24 GLY A 213 ALA A 214 LYS A 215 ASP A 218 SITE 2 AC1 24 LYS A 219 GLY A 237 GLY A 238 LEU A 256 SITE 3 AC1 24 GLY A 312 LEU A 313 ASN A 336 GLY A 337 SITE 4 AC1 24 GLY A 340 VAL A 341 GLU A 343 ASP A 374 SITE 5 AC1 24 THR A 375 MG A 502 HOH A 603 HOH A 634 SITE 6 AC1 24 HOH A 654 HOH A 700 HOH A 736 HOH A 765 SITE 1 AC2 6 ASN A 336 GLY A 372 ASP A 374 THR A 375 SITE 2 AC2 6 ADP A 501 HOH A 608 SITE 1 AC3 5 LYS A 85 ARG A 150 ALA A 151 HOH A 605 SITE 2 AC3 5 HOH A 810 CRYST1 35.721 105.570 50.002 90.00 97.76 90.00 P 1 21 1 2 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 0.027995 0.000000 0.003812 0.00000 SCALE2 0.000000 0.009472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020184 0.00000