PDB Short entry for 1T2E HEADER OXIDOREDUCTASE 21-APR-04 1T2E TITLE PLASMODIUM FALCIPARUM LACTATE DEHYDROGENASE S245A, A327P MUTANT TITLE 2 COMPLEXED WITH NADH AND OXAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-LACTATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LDH-P; COMPND 5 EC: 1.1.1.27; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_COMMON: MALARIA PARASITE P. FALCIPARUM; SOURCE 4 ORGANISM_TAXID: 5833; SOURCE 5 GENE: LDH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKK223 KEYWDS TERNARY COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMERON,J.READ,R.TRANTER,V.J.WINTER,R.B.SESSIONS,R.L.BRADY,L.VIVAS, AUTHOR 2 A.EASTON,H.KENDRICK,S.L.CROFT,D.BARROS,J.L.LAVANDERA,J.J.MARTIN, AUTHOR 3 F.RISCO,S.GARCIA-OCHOA,F.J.GAMO,L.SANZ,L.LEON,J.R.RUIZ,R.GABARRO, AUTHOR 4 A.MALLO,F.G.DE LAS HERAS REVDAT 6 23-AUG-23 1T2E 1 REMARK REVDAT 5 27-OCT-21 1T2E 1 REMARK SEQADV REVDAT 4 13-JUL-11 1T2E 1 VERSN REVDAT 3 24-FEB-09 1T2E 1 VERSN REVDAT 2 27-JUL-04 1T2E 1 JRNL REVDAT 1 11-MAY-04 1T2E 0 JRNL AUTH A.CAMERON,J.READ,R.TRANTER,V.J.WINTER,R.B.SESSIONS, JRNL AUTH 2 R.L.BRADY,L.VIVAS,A.EASTON,H.KENDRICK,S.L.CROFT,D.BARROS, JRNL AUTH 3 J.L.LAVANDERA,J.J.MARTIN,F.RISCO,S.GARCIA-OCHOA,F.J.GAMO, JRNL AUTH 4 L.SANZ,L.LEON,J.R.RUIZ,R.GABARRO,A.MALLO,F.G.DE LAS HERAS JRNL TITL IDENTIFICATION AND ACTIVITY OF A SERIES OF AZOLE-BASED JRNL TITL 2 COMPOUNDS WITH LACTATE DEHYDROGENASE-DIRECTED ANTI-MALARIAL JRNL TITL 3 ACTIVITY. JRNL REF J.BIOL.CHEM. V. 279 31429 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15117937 JRNL DOI 10.1074/JBC.M402433200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 23475 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1251 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1528 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2404 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -0.22000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.641 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2436 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3297 ; 2.375 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 4.249 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;14.330 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1750 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1568 ; 0.358 ; 0.300 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): 362 ; 0.159 ; 0.500 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): 96 ; 0.287 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 61 ; 0.942 ; 0.500 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): 1538 ; 1.157 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2483 ; 1.938 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 898 ; 3.371 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 815 ; 5.473 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25934 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1LDG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, HEPES, IMIDAZOLE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.53300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.66800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.85700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.53300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.66800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.85700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.53300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.66800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.85700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.53300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.66800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.85700 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 22270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 79.06600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.33600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 79.06600 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 85.33600 REMARK 350 BIOMT3 4 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 17 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 18 REMARK 475 PRO A 103B REMARK 475 GLY A 103C REMARK 475 PRO A 114 REMARK 475 LEU A 115 REMARK 475 ASN A 116 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 O HOH A 540 O HOH A 575 0.83 REMARK 500 OG SER A 103E CD LYS A 105B 2.01 REMARK 500 ND2 ASN A 296 O HOH A 576 2.02 REMARK 500 O HOH A 529 O HOH A 530 2.11 REMARK 500 O1N NAI A 336 O HOH A 566 2.19 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 O HOH A 560 O HOH A 571 6555 0.88 REMARK 500 O HOH A 574 O HOH A 574 2665 1.12 REMARK 500 O HOH A 455 O HOH A 551 4565 1.23 REMARK 500 NZ LYS A 118 O HOH A 554 6555 1.84 REMARK 500 CE LYS A 118 O HOH A 554 6555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 103A C PRO A 103B N -0.342 REMARK 500 LEU A 113 C PRO A 114 N -0.269 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 PRO A 103B C - N - CD ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP A 143 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 221 CB - CG - OD2 ANGL. DEV. = 6.0 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 57 -31.23 62.83 REMARK 500 ASN A 75 66.56 -150.84 REMARK 500 TYR A 247 -24.98 -145.48 REMARK 500 HIS A 330 36.04 -67.42 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 NAI A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXM A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LDG RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NADH AND OXAMATE REMARK 900 RELATED ID: 1T24 RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5-OXADIAZOLE-3- REMARK 900 CARBOXYLIC ACID REMARK 900 RELATED ID: 1T25 RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NADH AND 3-HYDROXYISOXAZOLE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 1T26 RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NADH AND 4-HYDROXY-1,2,5-THIADIAZOLE-3- REMARK 900 CARBOXYLIC ACID REMARK 900 RELATED ID: 1T2C RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NADH REMARK 900 RELATED ID: 1T2D RELATED DB: PDB REMARK 900 PFLDH COMPLEXED WITH NAD+ AND OXALATE REMARK 900 RELATED ID: 1T2F RELATED DB: PDB REMARK 900 HUMAN LDH COMPLEXED WITH NAD+ AND 4-HYDROXY-1,2,5-OXADIAZOLE-3- REMARK 900 CARBOXYLIC ACID DBREF 1T2E A 17 329 UNP Q27743 LDH1_PLAFD 1 316 SEQADV 1T2E ALA A 245 UNP Q27743 SER 234 ENGINEERED MUTATION SEQADV 1T2E PRO A 327 UNP Q27743 ALA 314 ENGINEERED MUTATION SEQADV 1T2E HIS A 330 UNP Q27743 EXPRESSION TAG SEQADV 1T2E HIS A 331 UNP Q27743 EXPRESSION TAG SEQADV 1T2E HIS A 332 UNP Q27743 EXPRESSION TAG SEQADV 1T2E HIS A 333 UNP Q27743 EXPRESSION TAG SEQADV 1T2E HIS A 334 UNP Q27743 EXPRESSION TAG SEQADV 1T2E HIS A 335 UNP Q27743 EXPRESSION TAG SEQRES 1 A 322 MET ALA PRO LYS ALA LYS ILE VAL LEU VAL GLY SER GLY SEQRES 2 A 322 MET ILE GLY GLY VAL MET ALA THR LEU ILE VAL GLN LYS SEQRES 3 A 322 ASN LEU GLY ASP VAL VAL LEU PHE ASP ILE VAL LYS ASN SEQRES 4 A 322 MET PRO HIS GLY LYS ALA LEU ASP THR SER HIS THR ASN SEQRES 5 A 322 VAL MET ALA TYR SER ASN CYS LYS VAL SER GLY SER ASN SEQRES 6 A 322 THR TYR ASP ASP LEU ALA GLY ALA ASP VAL VAL ILE VAL SEQRES 7 A 322 THR ALA GLY PHE THR LYS ALA PRO GLY LYS SER ASP LYS SEQRES 8 A 322 GLU TRP ASN ARG ASP ASP LEU LEU PRO LEU ASN ASN LYS SEQRES 9 A 322 ILE MET ILE GLU ILE GLY GLY HIS ILE LYS LYS ASN CYS SEQRES 10 A 322 PRO ASN ALA PHE ILE ILE VAL VAL THR ASN PRO VAL ASP SEQRES 11 A 322 VAL MET VAL GLN LEU LEU HIS GLN HIS SER GLY VAL PRO SEQRES 12 A 322 LYS ASN LYS ILE ILE GLY LEU GLY GLY VAL LEU ASP THR SEQRES 13 A 322 SER ARG LEU LYS TYR TYR ILE SER GLN LYS LEU ASN VAL SEQRES 14 A 322 CYS PRO ARG ASP VAL ASN ALA HIS ILE VAL GLY ALA HIS SEQRES 15 A 322 GLY ASN LYS MET VAL LEU LEU LYS ARG TYR ILE THR VAL SEQRES 16 A 322 GLY GLY ILE PRO LEU GLN GLU PHE ILE ASN ASN LYS LEU SEQRES 17 A 322 ILE SER ASP ALA GLU LEU GLU ALA ILE PHE ASP ARG THR SEQRES 18 A 322 VAL ASN THR ALA LEU GLU ILE VAL ASN LEU HIS ALA ALA SEQRES 19 A 322 PRO TYR VAL ALA PRO ALA ALA ALA ILE ILE GLU MET ALA SEQRES 20 A 322 GLU SER TYR LEU LYS ASP LEU LYS LYS VAL LEU ILE CYS SEQRES 21 A 322 SER THR LEU LEU GLU GLY GLN TYR GLY HIS SER ASP ILE SEQRES 22 A 322 PHE GLY GLY THR PRO VAL VAL LEU GLY ALA ASN GLY VAL SEQRES 23 A 322 GLU GLN VAL ILE GLU LEU GLN LEU ASN SER GLU GLU LYS SEQRES 24 A 322 ALA LYS PHE ASP GLU ALA ILE ALA GLU THR LYS ARG MET SEQRES 25 A 322 LYS PRO LEU ALA HIS HIS HIS HIS HIS HIS HET NAI A 336 44 HET OXM A 337 6 HET GOL A 338 6 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM OXM OXAMIC ACID HETNAM GOL GLYCEROL HETSYN NAI NADH HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAI C21 H29 N7 O14 P2 FORMUL 3 OXM C2 H3 N O3 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *242(H2 O) HELIX 1 1 GLY A 29 LYS A 43 1 14 HELIX 2 2 ASN A 57 HIS A 68 1 12 HELIX 3 3 HIS A 68 TYR A 73B 1 7 HELIX 4 4 THR A 84 ALA A 89 5 6 HELIX 5 5 ASN A 108 ASP A 111 5 4 HELIX 6 6 LEU A 112 CYS A 131 1 20 HELIX 7 7 PRO A 141 GLY A 154 1 14 HELIX 8 8 PRO A 156 ASN A 158 5 3 HELIX 9 9 GLY A 164 ASN A 181 1 18 HELIX 10 10 CYS A 183 ARG A 185 5 3 HELIX 11 11 LYS A 203 TYR A 205 5 3 HELIX 12 12 LEU A 210A ASN A 215 1 7 HELIX 13 13 SER A 220 ASN A 234 1 14 HELIX 14 14 ASN A 234 LEU A 242 1 9 HELIX 15 15 TYR A 247 LYS A 263 1 17 HELIX 16 16 GLN A 278 GLY A 280 5 3 HELIX 17 17 ASN A 308 HIS A 330 1 23 SHEET 1 A 6 VAL A 78 SER A 81 0 SHEET 2 A 6 ASP A 47 PHE A 52 1 N LEU A 51 O SER A 79 SHEET 3 A 6 LYS A 22 VAL A 26 1 N LEU A 25 O VAL A 50 SHEET 4 A 6 VAL A 93 VAL A 96 1 O ILE A 95 N VAL A 24 SHEET 5 A 6 PHE A 134 VAL A 137 1 O ILE A 136 N VAL A 96 SHEET 6 A 6 ILE A 160 GLY A 162 1 O ILE A 161 N VAL A 137 SHEET 1 B 3 VAL A 187 ASN A 188 0 SHEET 2 B 3 THR A 207 VAL A 208 -1 O THR A 207 N ASN A 188 SHEET 3 B 3 ILE A 209C PRO A 209D-1 O ILE A 209C N VAL A 208 SHEET 1 C 2 ILE A 191 VAL A 192 0 SHEET 2 C 2 VAL A 200 LEU A 201 -1 O VAL A 200 N VAL A 192 SHEET 1 D 3 LYS A 267 GLU A 276 0 SHEET 2 D 3 SER A 282 GLY A 294 -1 O ILE A 285 N LEU A 275 SHEET 3 D 3 GLY A 297 VAL A 302 -1 O GLU A 299 N VAL A 292 CISPEP 1 ASN A 140 PRO A 141 0 -2.70 SITE 1 AC1 31 GLY A 27 GLY A 29 MET A 30 ILE A 31 SITE 2 AC1 31 PHE A 52 ASP A 53 ILE A 54 VAL A 55 SITE 3 AC1 31 TYR A 85 THR A 97 ALA A 98 GLY A 99 SITE 4 AC1 31 PHE A 100 THR A 101 VAL A 138 THR A 139 SITE 5 AC1 31 ASN A 140 VAL A 142 LEU A 163 LEU A 167 SITE 6 AC1 31 HIS A 195 PRO A 250 OXM A 337 HOH A 355 SITE 7 AC1 31 HOH A 359 HOH A 396 HOH A 408 HOH A 425 SITE 8 AC1 31 HOH A 493 HOH A 512 HOH A 566 SITE 1 AC2 9 ARG A 109 ASN A 140 LEU A 167 ARG A 171 SITE 2 AC2 9 HIS A 195 ALA A 236 PRO A 246 NAI A 336 SITE 3 AC2 9 HOH A 512 SITE 1 AC3 11 THR A 169 LYS A 173 ASN A 188 ALA A 189 SITE 2 AC3 11 HIS A 190 GLY A 209A VAL A 268 ILE A 270 SITE 3 AC3 11 HOH A 350 HOH A 397 HOH A 398 CRYST1 79.066 85.336 89.714 90.00 90.00 90.00 I 2 2 2 8 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 0.012648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011147 0.00000