HEADER OXIDOREDUCTASE 30-MAR-05 1X0V TITLE CRYSTAL STRUCTURE OF HOMO SAPIEN GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD+], CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GPD-C, GPDH-C; COMPND 5 EC: 1.1.1.8; COMPND 6 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: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DE3(BL21); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS TWO INDEPENDENT DOMAINS, GXGXXG MOTIF, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.RAO,X.OU REVDAT 3 30-OCT-24 1X0V 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1X0V 1 VERSN REVDAT 1 11-APR-06 1X0V 0 JRNL AUTH X.OU,C.JI,X.HAN,X.ZHAO,X.LI,Y.MAO,L.L.WONG,M.BARTLAM,Z.RAO JRNL TITL CRYSTAL STRUCTURES OF HUMAN GLYCEROL 3-PHOSPHATE JRNL TITL 2 DEHYDROGENASE 1 (GPD1) JRNL REF J.MOL.BIOL. V. 357 858 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16460752 JRNL DOI 10.1016/J.JMB.2005.12.074 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 85858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 8447 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 651 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X0V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000024238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798, 0.9800, 0.900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-SODIUM CITRATE DIHYDRATE, REMARK 280 0.5M AMMONIUM SULFATE, 1.0M LITHIUM SULFATE MONOHYDORATE, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 77.71800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.74400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.74400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 116.57700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.74400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.74400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.85900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.74400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.74400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 116.57700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.74400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.74400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.85900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 77.71800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -178.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -191.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 -56.74400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 -56.74400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -38.85900 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MSE A 1 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 ASP B 103 C GLN B 104 N 0.231 REMARK 500 ARG B 139 C LEU B 140 N 0.243 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 GLY A 128 N - CA - C ANGL. DEV. = -19.3 DEGREES REMARK 500 PRO A 143 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 PRO A 320 C - N - CA ANGL. DEV. = 9.6 DEGREES REMARK 500 ASP B 103 CB - CA - C ANGL. DEV. = 15.6 DEGREES REMARK 500 GLU B 138 CA - C - N ANGL. DEV. = 16.6 DEGREES REMARK 500 GLU B 138 O - C - N ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG B 139 C - N - CA ANGL. DEV. = 21.6 DEGREES REMARK 500 ARG B 139 CA - C - N ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG B 139 O - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 LEU B 147 CA - CB - CG ANGL. DEV. = 14.4 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 SER A 11 27.24 -148.85 REMARK 500 VAL A 92 58.15 -151.84 REMARK 500 PRO A 126 100.00 -59.69 REMARK 500 LEU A 291 -15.80 -145.82 REMARK 500 SER B 11 30.28 -152.23 REMARK 500 ASN B 127 -28.97 101.38 REMARK 500 ASN B 293 18.83 40.76 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 ASP B 103 -15.46 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 SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1014 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WPQ RELATED DB: PDB REMARK 900 THE SAME PRTEIN COMPLEXED WITH NAD AND DIHYDROXYACETONE REMARK 900 RELATED ID: 1X0X RELATED DB: PDB REMARK 900 THE SAME PRTEIN COMPLEXED WITH NAD DBREF 1X0V A 1 349 UNP P21695 GPDA_HUMAN 1 348 DBREF 1X0V B 1 349 UNP P21695 GPDA_HUMAN 1 348 SEQADV 1X0V GLY A -4 UNP P21695 CLONING ARTIFACT SEQADV 1X0V PRO A -3 UNP P21695 CLONING ARTIFACT SEQADV 1X0V LEU A -2 UNP P21695 CLONING ARTIFACT SEQADV 1X0V GLY A -1 UNP P21695 CLONING ARTIFACT SEQADV 1X0V SER A 0 UNP P21695 CLONING ARTIFACT SEQADV 1X0V MSE A 1 UNP P21695 MET 1 MODIFIED RESIDUE SEQADV 1X0V MSE A 38 UNP P21695 MET 37 MODIFIED RESIDUE SEQADV 1X0V MSE A 144 UNP P21695 MET 143 MODIFIED RESIDUE SEQADV 1X0V MSE A 148 UNP P21695 MET 147 MODIFIED RESIDUE SEQADV 1X0V MSE A 181 UNP P21695 MET 180 MODIFIED RESIDUE SEQADV 1X0V MSE A 233 UNP P21695 MET 232 MODIFIED RESIDUE SEQADV 1X0V MSE A 235 UNP P21695 MET 234 MODIFIED RESIDUE SEQADV 1X0V MSE A 323 UNP P21695 MET 322 MODIFIED RESIDUE SEQADV 1X0V MSE A 349 UNP P21695 MET 348 MODIFIED RESIDUE SEQADV 1X0V GLY B -4 UNP P21695 CLONING ARTIFACT SEQADV 1X0V PRO B -3 UNP P21695 CLONING ARTIFACT SEQADV 1X0V LEU B -2 UNP P21695 CLONING ARTIFACT SEQADV 1X0V GLY B -1 UNP P21695 CLONING ARTIFACT SEQADV 1X0V SER B 0 UNP P21695 CLONING ARTIFACT SEQADV 1X0V MSE B 1 UNP P21695 MET 1 MODIFIED RESIDUE SEQADV 1X0V MSE B 38 UNP P21695 MET 37 MODIFIED RESIDUE SEQADV 1X0V MSE B 144 UNP P21695 MET 143 MODIFIED RESIDUE SEQADV 1X0V MSE B 148 UNP P21695 MET 147 MODIFIED RESIDUE SEQADV 1X0V MSE B 181 UNP P21695 MET 180 MODIFIED RESIDUE SEQADV 1X0V MSE B 233 UNP P21695 MET 232 MODIFIED RESIDUE SEQADV 1X0V MSE B 235 UNP P21695 MET 234 MODIFIED RESIDUE SEQADV 1X0V MSE B 323 UNP P21695 MET 322 MODIFIED RESIDUE SEQADV 1X0V MSE B 349 UNP P21695 MET 348 MODIFIED RESIDUE SEQRES 1 A 354 GLY PRO LEU GLY SER MSE ALA SER LYS LYS VAL CYS ILE SEQRES 2 A 354 VAL GLY SER GLY ASN TRP GLY SER ALA ILE ALA LYS ILE SEQRES 3 A 354 VAL GLY GLY ASN ALA ALA GLN LEU ALA GLN PHE ASP PRO SEQRES 4 A 354 ARG VAL THR MSE TRP VAL PHE GLU GLU ASP ILE GLY GLY SEQRES 5 A 354 LYS LYS LEU THR GLU ILE ILE ASN THR GLN HIS GLU ASN SEQRES 6 A 354 VAL LYS TYR LEU PRO GLY HIS LYS LEU PRO PRO ASN VAL SEQRES 7 A 354 VAL ALA VAL PRO ASP VAL VAL GLN ALA ALA GLU ASP ALA SEQRES 8 A 354 ASP ILE LEU ILE PHE VAL VAL PRO HIS GLN PHE ILE GLY SEQRES 9 A 354 LYS ILE CYS ASP GLN LEU LYS GLY HIS LEU LYS ALA ASN SEQRES 10 A 354 ALA THR GLY ILE SER LEU ILE LYS GLY VAL ASP GLU GLY SEQRES 11 A 354 PRO ASN GLY LEU LYS LEU ILE SER GLU VAL ILE GLY GLU SEQRES 12 A 354 ARG LEU GLY ILE PRO MSE SER VAL LEU MSE GLY ALA ASN SEQRES 13 A 354 ILE ALA SER GLU VAL ALA ASP GLU LYS PHE CYS GLU THR SEQRES 14 A 354 THR ILE GLY CYS LYS ASP PRO ALA GLN GLY GLN LEU LEU SEQRES 15 A 354 LYS GLU LEU MSE GLN THR PRO ASN PHE ARG ILE THR VAL SEQRES 16 A 354 VAL GLN GLU VAL ASP THR VAL GLU ILE CYS GLY ALA LEU SEQRES 17 A 354 LYS ASN VAL VAL ALA VAL GLY ALA GLY PHE CYS ASP GLY SEQRES 18 A 354 LEU GLY PHE GLY ASP ASN THR LYS ALA ALA VAL ILE ARG SEQRES 19 A 354 LEU GLY LEU MSE GLU MSE ILE ALA PHE ALA LYS LEU PHE SEQRES 20 A 354 CYS SER GLY PRO VAL SER SER ALA THR PHE LEU GLU SER SEQRES 21 A 354 CYS GLY VAL ALA ASP LEU ILE THR THR CYS TYR GLY GLY SEQRES 22 A 354 ARG ASN ARG LYS VAL ALA GLU ALA PHE ALA ARG THR GLY SEQRES 23 A 354 LYS SER ILE GLU GLN LEU GLU LYS GLU LEU LEU ASN GLY SEQRES 24 A 354 GLN LYS LEU GLN GLY PRO GLU THR ALA ARG GLU LEU TYR SEQRES 25 A 354 SER ILE LEU GLN HIS LYS GLY LEU VAL ASP LYS PHE PRO SEQRES 26 A 354 LEU PHE MSE ALA VAL TYR LYS VAL CYS TYR GLU GLY GLN SEQRES 27 A 354 PRO VAL GLY GLU PHE ILE HIS CYS LEU GLN ASN HIS PRO SEQRES 28 A 354 GLU HIS MSE SEQRES 1 B 354 GLY PRO LEU GLY SER MSE ALA SER LYS LYS VAL CYS ILE SEQRES 2 B 354 VAL GLY SER GLY ASN TRP GLY SER ALA ILE ALA LYS ILE SEQRES 3 B 354 VAL GLY GLY ASN ALA ALA GLN LEU ALA GLN PHE ASP PRO SEQRES 4 B 354 ARG VAL THR MSE TRP VAL PHE GLU GLU ASP ILE GLY GLY SEQRES 5 B 354 LYS LYS LEU THR GLU ILE ILE ASN THR GLN HIS GLU ASN SEQRES 6 B 354 VAL LYS TYR LEU PRO GLY HIS LYS LEU PRO PRO ASN VAL SEQRES 7 B 354 VAL ALA VAL PRO ASP VAL VAL GLN ALA ALA GLU ASP ALA SEQRES 8 B 354 ASP ILE LEU ILE PHE VAL VAL PRO HIS GLN PHE ILE GLY SEQRES 9 B 354 LYS ILE CYS ASP GLN LEU LYS GLY HIS LEU LYS ALA ASN SEQRES 10 B 354 ALA THR GLY ILE SER LEU ILE LYS GLY VAL ASP GLU GLY SEQRES 11 B 354 PRO ASN GLY LEU LYS LEU ILE SER GLU VAL ILE GLY GLU SEQRES 12 B 354 ARG LEU GLY ILE PRO MSE SER VAL LEU MSE GLY ALA ASN SEQRES 13 B 354 ILE ALA SER GLU VAL ALA ASP GLU LYS PHE CYS GLU THR SEQRES 14 B 354 THR ILE GLY CYS LYS ASP PRO ALA GLN GLY GLN LEU LEU SEQRES 15 B 354 LYS GLU LEU MSE GLN THR PRO ASN PHE ARG ILE THR VAL SEQRES 16 B 354 VAL GLN GLU VAL ASP THR VAL GLU ILE CYS GLY ALA LEU SEQRES 17 B 354 LYS ASN VAL VAL ALA VAL GLY ALA GLY PHE CYS ASP GLY SEQRES 18 B 354 LEU GLY PHE GLY ASP ASN THR LYS ALA ALA VAL ILE ARG SEQRES 19 B 354 LEU GLY LEU MSE GLU MSE ILE ALA PHE ALA LYS LEU PHE SEQRES 20 B 354 CYS SER GLY PRO VAL SER SER ALA THR PHE LEU GLU SER SEQRES 21 B 354 CYS GLY VAL ALA ASP LEU ILE THR THR CYS TYR GLY GLY SEQRES 22 B 354 ARG ASN ARG LYS VAL ALA GLU ALA PHE ALA ARG THR GLY SEQRES 23 B 354 LYS SER ILE GLU GLN LEU GLU LYS GLU LEU LEU ASN GLY SEQRES 24 B 354 GLN LYS LEU GLN GLY PRO GLU THR ALA ARG GLU LEU TYR SEQRES 25 B 354 SER ILE LEU GLN HIS LYS GLY LEU VAL ASP LYS PHE PRO SEQRES 26 B 354 LEU PHE MSE ALA VAL TYR LYS VAL CYS TYR GLU GLY GLN SEQRES 27 B 354 PRO VAL GLY GLU PHE ILE HIS CYS LEU GLN ASN HIS PRO SEQRES 28 B 354 GLU HIS MSE MODRES 1X0V MSE A 38 MET SELENOMETHIONINE MODRES 1X0V MSE A 144 MET SELENOMETHIONINE MODRES 1X0V MSE A 148 MET SELENOMETHIONINE MODRES 1X0V MSE A 181 MET SELENOMETHIONINE MODRES 1X0V MSE A 233 MET SELENOMETHIONINE MODRES 1X0V MSE A 235 MET SELENOMETHIONINE MODRES 1X0V MSE A 323 MET SELENOMETHIONINE MODRES 1X0V MSE A 349 MET SELENOMETHIONINE MODRES 1X0V MSE B 1 MET SELENOMETHIONINE MODRES 1X0V MSE B 38 MET SELENOMETHIONINE MODRES 1X0V MSE B 144 MET SELENOMETHIONINE MODRES 1X0V MSE B 148 MET SELENOMETHIONINE MODRES 1X0V MSE B 181 MET SELENOMETHIONINE MODRES 1X0V MSE B 233 MET SELENOMETHIONINE MODRES 1X0V MSE B 235 MET SELENOMETHIONINE MODRES 1X0V MSE B 323 MET SELENOMETHIONINE MODRES 1X0V MSE B 349 MET SELENOMETHIONINE HET MSE A 38 8 HET MSE A 144 8 HET MSE A 148 8 HET MSE A 181 8 HET MSE A 233 8 HET MSE A 235 8 HET MSE A 323 8 HET MSE A 349 9 HET MSE B 1 8 HET MSE B 38 8 HET MSE B 144 8 HET MSE B 148 8 HET MSE B 181 8 HET MSE B 233 8 HET MSE B 235 8 HET MSE B 323 8 HET MSE B 349 9 HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1003 5 HET SO4 A1004 5 HET SO4 A1007 5 HET SO4 A1009 5 HET SO4 A1012 5 HET SO4 A1013 5 HET SO4 B1005 5 HET SO4 B1006 5 HET SO4 B1008 5 HET SO4 B1010 5 HET SO4 B1011 5 HET SO4 B1014 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 17(C5 H11 N O2 SE) FORMUL 3 SO4 14(O4 S 2-) FORMUL 17 HOH *651(H2 O) HELIX 1 1 GLY A 12 LEU A 29 1 18 HELIX 2 2 LYS A 49 HIS A 58 1 10 HELIX 3 3 ASP A 78 GLU A 84 1 7 HELIX 4 4 PRO A 94 GLN A 96 5 3 HELIX 5 5 PHE A 97 LYS A 106 1 10 HELIX 6 6 LEU A 131 GLY A 141 1 11 HELIX 7 7 ILE A 152 ASP A 158 1 7 HELIX 8 8 ASP A 170 GLN A 182 1 13 HELIX 9 9 GLU A 193 LEU A 217 1 25 HELIX 10 10 GLY A 220 CYS A 243 1 24 HELIX 11 11 SER A 248 GLU A 254 5 7 HELIX 12 12 GLY A 257 GLY A 268 1 12 HELIX 13 13 GLY A 268 GLY A 281 1 14 HELIX 14 14 SER A 283 LEU A 292 1 10 HELIX 15 15 LEU A 297 GLY A 314 1 18 HELIX 16 16 LEU A 315 LYS A 318 5 4 HELIX 17 17 PHE A 319 GLU A 331 1 13 HELIX 18 18 PRO A 334 GLU A 337 5 4 HELIX 19 19 PHE A 338 ASN A 344 1 7 HELIX 20 20 GLY B 12 LEU B 29 1 18 HELIX 21 21 LEU B 50 HIS B 58 1 9 HELIX 22 22 ASP B 78 GLU B 84 1 7 HELIX 23 23 PRO B 94 GLN B 96 5 3 HELIX 24 24 PHE B 97 LYS B 106 1 10 HELIX 25 25 LEU B 131 GLY B 141 1 11 HELIX 26 26 ILE B 152 ASP B 158 1 7 HELIX 27 27 ASP B 170 GLN B 182 1 13 HELIX 28 28 GLU B 193 LEU B 217 1 25 HELIX 29 29 GLY B 220 CYS B 243 1 24 HELIX 30 30 SER B 248 GLU B 254 5 7 HELIX 31 31 GLY B 257 GLY B 268 1 12 HELIX 32 32 GLY B 268 GLY B 281 1 14 HELIX 33 33 SER B 283 LEU B 292 1 10 HELIX 34 34 LEU B 297 GLY B 314 1 18 HELIX 35 35 LEU B 315 LYS B 318 5 4 HELIX 36 36 PHE B 319 GLU B 331 1 13 HELIX 37 37 PRO B 334 PHE B 338 5 5 HELIX 38 38 ILE B 339 ASN B 344 1 6 SHEET 1 A 8 VAL A 73 VAL A 76 0 SHEET 2 A 8 PHE A 32 TRP A 39 1 N MSE A 38 O VAL A 74 SHEET 3 A 8 LYS A 4 VAL A 9 1 N ILE A 8 O THR A 37 SHEET 4 A 8 ILE A 88 PHE A 91 1 O ILE A 90 N VAL A 9 SHEET 5 A 8 THR A 114 SER A 117 1 O ILE A 116 N PHE A 91 SHEET 6 A 8 MSE A 144 MSE A 148 1 O SER A 145 N SER A 117 SHEET 7 A 8 CYS A 162 GLY A 167 -1 O GLY A 167 N VAL A 146 SHEET 8 A 8 PHE A 186 VAL A 191 1 O VAL A 191 N ILE A 166 SHEET 1 B 8 VAL B 73 VAL B 76 0 SHEET 2 B 8 PHE B 32 TRP B 39 1 N MSE B 38 O VAL B 76 SHEET 3 B 8 LYS B 4 VAL B 9 1 N ILE B 8 O THR B 37 SHEET 4 B 8 ILE B 88 PHE B 91 1 O ILE B 90 N CYS B 7 SHEET 5 B 8 THR B 114 SER B 117 1 O ILE B 116 N PHE B 91 SHEET 6 B 8 MSE B 144 MSE B 148 1 O SER B 145 N SER B 117 SHEET 7 B 8 CYS B 162 GLY B 167 -1 O THR B 165 N MSE B 148 SHEET 8 B 8 PHE B 186 VAL B 191 1 O VAL B 191 N ILE B 166 SHEET 1 C 2 ASP B 44 ILE B 45 0 SHEET 2 C 2 LYS B 48 LYS B 49 -1 O LYS B 48 N ILE B 45 LINK C THR A 37 N MSE A 38 1555 1555 1.32 LINK C MSE A 38 N TRP A 39 1555 1555 1.33 LINK C PRO A 143 N MSE A 144 1555 1555 1.34 LINK C MSE A 144 N SER A 145 1555 1555 1.34 LINK C LEU A 147 N MSE A 148 1555 1555 1.33 LINK C MSE A 148 N GLY A 149 1555 1555 1.33 LINK C LEU A 180 N MSE A 181 1555 1555 1.34 LINK C MSE A 181 N GLN A 182 1555 1555 1.32 LINK C LEU A 232 N MSE A 233 1555 1555 1.33 LINK C MSE A 233 N GLU A 234 1555 1555 1.33 LINK C GLU A 234 N MSE A 235 1555 1555 1.34 LINK C MSE A 235 N ILE A 236 1555 1555 1.34 LINK C PHE A 322 N MSE A 323 1555 1555 1.33 LINK C MSE A 323 N ALA A 324 1555 1555 1.34 LINK C HIS A 348 N MSE A 349 1555 1555 1.33 LINK C MSE B 1 N ALA B 2 1555 1555 1.33 LINK C THR B 37 N MSE B 38 1555 1555 1.33 LINK C MSE B 38 N TRP B 39 1555 1555 1.33 LINK C PRO B 143 N MSE B 144 1555 1555 1.34 LINK C MSE B 144 N SER B 145 1555 1555 1.33 LINK C LEU B 147 N MSE B 148 1555 1555 1.33 LINK C MSE B 148 N GLY B 149 1555 1555 1.33 LINK C LEU B 180 N MSE B 181 1555 1555 1.33 LINK C MSE B 181 N GLN B 182 1555 1555 1.33 LINK C LEU B 232 N MSE B 233 1555 1555 1.33 LINK C MSE B 233 N GLU B 234 1555 1555 1.33 LINK C GLU B 234 N MSE B 235 1555 1555 1.33 LINK C MSE B 235 N ILE B 236 1555 1555 1.33 LINK C PHE B 322 N MSE B 323 1555 1555 1.33 LINK C MSE B 323 N ALA B 324 1555 1555 1.33 LINK C HIS B 348 N MSE B 349 1555 1555 1.33 SITE 1 AC1 4 LYS A 20 HIS A 67 LYS A 68 HOH A1245 SITE 1 AC2 2 LYS B 68 SO4 B1010 SITE 1 AC3 5 ASN A 13 TRP A 14 ARG A 269 HOH A1058 SITE 2 AC3 5 HOH A1173 SITE 1 AC4 5 ARG A 271 HOH A1073 HOH A1222 HOH A1290 SITE 2 AC4 5 HOH A1327 SITE 1 AC5 7 GLY B 12 ASN B 13 TRP B 14 HOH B1035 SITE 2 AC5 7 HOH B1168 HOH B1178 HOH B1295 SITE 1 AC6 10 LYS B 204 THR B 264 GLY B 268 ARG B 269 SITE 2 AC6 10 ASN B 270 HOH B1028 HOH B1038 HOH B1088 SITE 3 AC6 10 HOH B1119 HOH B1315 SITE 1 AC7 6 LYS A 178 GLN A 182 ARG A 187 HOH A1049 SITE 2 AC7 6 HOH A1115 HOH A1314 SITE 1 AC8 4 PRO B 346 GLU B 347 HIS B 348 HOH B1235 SITE 1 AC9 11 LYS A 204 ASN A 205 THR A 264 GLY A 268 SITE 2 AC9 11 ARG A 269 ASN A 270 GLN A 298 HOH A1028 SITE 3 AC9 11 HOH A1043 HOH A1153 HOH A1165 SITE 1 BC1 4 SO4 A1002 LYS B 20 GLY B 66 HIS B 67 SITE 1 BC2 4 LYS B 240 SER B 248 SER B 249 HOH B1258 SITE 1 BC3 4 LYS A 240 SER A 248 SER A 249 HOH A1114 SITE 1 BC4 4 PRO A 346 GLU A 347 HIS A 348 HOH A1307 SITE 1 BC5 4 LYS B 178 GLN B 182 ARG B 187 HOH B1146 CRYST1 113.488 113.488 155.436 90.00 90.00 90.00 P 43 21 2 16 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 0.008812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006434 0.00000