HEADER OXIDOREDUCTASE 25-AUG-14 3WYC TITLE STRUCTURE OF A MESO-DIAMINOPIMELATE DEHYDROGENASE IN COMPLEX WITH NADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESO-DIAMINOPIMELATE D-DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAPDH, MESO-DAP DEHYDROGENASE; COMPND 5 EC: 1.4.1.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UREIBACILLUS THERMOSPHAERICUS; SOURCE 3 ORGANISM_TAXID: 51173; SOURCE 4 GENE: DDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SAKURABA,H.AKITA,T.OHSHIMA REVDAT 4 20-MAR-24 3WYC 1 REMARK SEQADV REVDAT 3 22-NOV-17 3WYC 1 REMARK REVDAT 2 20-MAY-15 3WYC 1 JRNL REVDAT 1 06-MAY-15 3WYC 0 JRNL AUTH H.AKITA,T.SETO,T.OHSHIMA,H.SAKURABA JRNL TITL STRUCTURAL INSIGHT INTO THE THERMOSTABLE NADP(+)-DEPENDENT JRNL TITL 2 MESO-DIAMINOPIMELATE DEHYDROGENASE FROM UREIBACILLUS JRNL TITL 3 THERMOSPHAERICUS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1136 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25945579 JRNL DOI 10.1107/S1399004715003673 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 66282 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3365 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4630 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 251 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 152 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -1.16000 REMARK 3 B12 (A**2) : 0.36000 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): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.339 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5348 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4978 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7266 ; 2.067 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11478 ; 0.938 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 652 ; 6.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;36.379 ;24.480 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 864 ;15.408 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;15.584 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 794 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6040 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1222 ; 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): 2614 ; 3.237 ; 3.142 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2613 ; 3.214 ; 3.141 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3264 ; 4.080 ; 4.687 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3WYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000096946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-13 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRISODIUM CITRATE DIHYDRATE, TES, REMARK 280 NADP, D-LYS, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 61.51050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.51310 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.43400 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 61.51050 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 35.51310 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.43400 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 61.51050 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 35.51310 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.43400 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.02621 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 128.86800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 71.02621 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 128.86800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 71.02621 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 128.86800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 1 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 MET B 1 REMARK 465 HIS B 329 REMARK 465 HIS B 330 REMARK 465 HIS B 331 REMARK 465 HIS B 332 REMARK 465 HIS B 333 REMARK 465 HIS B 334 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 328 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 328 CG CD NE CZ NH1 NH2 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 223 -22.54 83.75 REMARK 500 ASN B 223 -19.11 84.03 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 NAP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NES A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NES A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NES B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NES B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WYB RELATED DB: PDB DBREF 3WYC A 1 326 UNP G1UII1 DAPDH_URETH 1 326 DBREF 3WYC B 1 326 UNP G1UII1 DAPDH_URETH 1 326 SEQADV 3WYC THR A 327 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC ARG A 328 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 329 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 330 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 331 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 332 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 333 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS A 334 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC THR B 327 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC ARG B 328 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 329 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 330 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 331 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 332 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 333 UNP G1UII1 EXPRESSION TAG SEQADV 3WYC HIS B 334 UNP G1UII1 EXPRESSION TAG SEQRES 1 A 334 MET SER LYS ILE ARG ILE GLY ILE VAL GLY TYR GLY ASN SEQRES 2 A 334 LEU GLY ARG GLY VAL GLU ALA ALA ILE GLN GLN ASN PRO SEQRES 3 A 334 ASP MET GLU LEU VAL ALA VAL PHE THR ARG ARG ASP PRO SEQRES 4 A 334 LYS THR VAL ALA VAL LYS SER ASN VAL LYS VAL LEU HIS SEQRES 5 A 334 VAL ASP ASP ALA GLN SER TYR LYS ASP GLU ILE ASP VAL SEQRES 6 A 334 MET ILE LEU CYS GLY GLY SER ALA THR ASP LEU PRO GLU SEQRES 7 A 334 GLN GLY PRO TYR PHE ALA GLN TYR PHE ASN THR ILE ASP SEQRES 8 A 334 SER PHE ASP THR HIS ALA ARG ILE PRO ASP TYR PHE ASP SEQRES 9 A 334 ALA VAL ASN ALA ALA ALA GLU GLN SER GLY LYS VAL ALA SEQRES 10 A 334 ILE ILE SER VAL GLY TRP ASP PRO GLY LEU PHE SER LEU SEQRES 11 A 334 ASN ARG LEU LEU GLY GLU VAL VAL LEU PRO VAL GLY ASN SEQRES 12 A 334 THR TYR THR PHE TRP GLY LYS GLY VAL SER GLN GLY HIS SEQRES 13 A 334 SER ASP ALA ILE ARG ARG ILE GLN GLY VAL LYS ASN ALA SEQRES 14 A 334 VAL GLN TYR THR ILE PRO ILE ASP GLU ALA VAL ASN ARG SEQRES 15 A 334 VAL ARG SER GLY GLU ASN PRO GLU LEU SER THR ARG GLU SEQRES 16 A 334 LYS HIS ALA ARG GLU CYS PHE VAL VAL LEU GLU GLU GLY SEQRES 17 A 334 ALA ASP PRO ALA LYS VAL GLU HIS GLU ILE LYS THR MET SEQRES 18 A 334 PRO ASN TYR PHE ASP GLU TYR ASP THR THR VAL HIS PHE SEQRES 19 A 334 ILE SER GLU GLU GLU LEU LYS GLN ASN HIS SER GLY MET SEQRES 20 A 334 PRO HIS GLY GLY PHE VAL ILE ARG SER GLY LYS SER ASP SEQRES 21 A 334 GLU GLY HIS LYS GLN ILE ILE GLU PHE SER LEU ASN LEU SEQRES 22 A 334 GLU SER ASN PRO MET PHE THR SER SER ALA LEU VAL ALA SEQRES 23 A 334 TYR ALA ARG ALA ALA TYR ARG LEU SER GLN ASN GLY ASP SEQRES 24 A 334 LYS GLY ALA LYS THR VAL PHE ASP ILE PRO PHE GLY LEU SEQRES 25 A 334 LEU SER PRO LYS SER PRO GLU ASP LEU ARG LYS GLU LEU SEQRES 26 A 334 LEU THR ARG HIS HIS HIS HIS HIS HIS SEQRES 1 B 334 MET SER LYS ILE ARG ILE GLY ILE VAL GLY TYR GLY ASN SEQRES 2 B 334 LEU GLY ARG GLY VAL GLU ALA ALA ILE GLN GLN ASN PRO SEQRES 3 B 334 ASP MET GLU LEU VAL ALA VAL PHE THR ARG ARG ASP PRO SEQRES 4 B 334 LYS THR VAL ALA VAL LYS SER ASN VAL LYS VAL LEU HIS SEQRES 5 B 334 VAL ASP ASP ALA GLN SER TYR LYS ASP GLU ILE ASP VAL SEQRES 6 B 334 MET ILE LEU CYS GLY GLY SER ALA THR ASP LEU PRO GLU SEQRES 7 B 334 GLN GLY PRO TYR PHE ALA GLN TYR PHE ASN THR ILE ASP SEQRES 8 B 334 SER PHE ASP THR HIS ALA ARG ILE PRO ASP TYR PHE ASP SEQRES 9 B 334 ALA VAL ASN ALA ALA ALA GLU GLN SER GLY LYS VAL ALA SEQRES 10 B 334 ILE ILE SER VAL GLY TRP ASP PRO GLY LEU PHE SER LEU SEQRES 11 B 334 ASN ARG LEU LEU GLY GLU VAL VAL LEU PRO VAL GLY ASN SEQRES 12 B 334 THR TYR THR PHE TRP GLY LYS GLY VAL SER GLN GLY HIS SEQRES 13 B 334 SER ASP ALA ILE ARG ARG ILE GLN GLY VAL LYS ASN ALA SEQRES 14 B 334 VAL GLN TYR THR ILE PRO ILE ASP GLU ALA VAL ASN ARG SEQRES 15 B 334 VAL ARG SER GLY GLU ASN PRO GLU LEU SER THR ARG GLU SEQRES 16 B 334 LYS HIS ALA ARG GLU CYS PHE VAL VAL LEU GLU GLU GLY SEQRES 17 B 334 ALA ASP PRO ALA LYS VAL GLU HIS GLU ILE LYS THR MET SEQRES 18 B 334 PRO ASN TYR PHE ASP GLU TYR ASP THR THR VAL HIS PHE SEQRES 19 B 334 ILE SER GLU GLU GLU LEU LYS GLN ASN HIS SER GLY MET SEQRES 20 B 334 PRO HIS GLY GLY PHE VAL ILE ARG SER GLY LYS SER ASP SEQRES 21 B 334 GLU GLY HIS LYS GLN ILE ILE GLU PHE SER LEU ASN LEU SEQRES 22 B 334 GLU SER ASN PRO MET PHE THR SER SER ALA LEU VAL ALA SEQRES 23 B 334 TYR ALA ARG ALA ALA TYR ARG LEU SER GLN ASN GLY ASP SEQRES 24 B 334 LYS GLY ALA LYS THR VAL PHE ASP ILE PRO PHE GLY LEU SEQRES 25 B 334 LEU SER PRO LYS SER PRO GLU ASP LEU ARG LYS GLU LEU SEQRES 26 B 334 LEU THR ARG HIS HIS HIS HIS HIS HIS HET NAP A1001 48 HET NES A1002 14 HET NES A1003 14 HET NAP B1001 48 HET NES B1002 14 HET NES B1003 14 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM NES 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 NES ETHANESULFONIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 NES 4(C6 H15 N O6 S) FORMUL 9 HOH *387(H2 O) HELIX 1 1 GLY A 12 GLN A 23 1 12 HELIX 2 2 ASP A 38 VAL A 42 5 5 HELIX 3 3 ASP A 54 LYS A 60 5 7 HELIX 4 4 THR A 74 GLN A 85 1 12 HELIX 5 5 THR A 95 ALA A 97 5 3 HELIX 6 6 ARG A 98 GLY A 114 1 17 HELIX 7 7 GLY A 126 LEU A 139 1 14 HELIX 8 8 SER A 153 ARG A 162 1 10 HELIX 9 9 ILE A 176 SER A 185 1 10 HELIX 10 10 SER A 192 LYS A 196 1 5 HELIX 11 11 ASP A 210 THR A 220 1 11 HELIX 12 12 SER A 236 HIS A 244 1 9 HELIX 13 13 SER A 275 ASN A 297 1 23 HELIX 14 14 THR A 304 ILE A 308 5 5 HELIX 15 15 PRO A 309 SER A 314 5 6 HELIX 16 16 SER A 317 LEU A 326 1 10 HELIX 17 17 GLY B 12 GLN B 23 1 12 HELIX 18 18 ASP B 38 VAL B 42 5 5 HELIX 19 19 ASP B 54 LYS B 60 5 7 HELIX 20 20 THR B 74 ALA B 84 1 11 HELIX 21 21 THR B 95 ALA B 97 5 3 HELIX 22 22 ARG B 98 GLY B 114 1 17 HELIX 23 23 GLY B 126 LEU B 139 1 14 HELIX 24 24 SER B 153 ARG B 162 1 10 HELIX 25 25 ILE B 176 SER B 185 1 10 HELIX 26 26 SER B 192 LYS B 196 1 5 HELIX 27 27 ASP B 210 THR B 220 1 11 HELIX 28 28 SER B 236 HIS B 244 1 9 HELIX 29 29 SER B 275 ASN B 297 1 23 HELIX 30 30 THR B 304 ILE B 308 5 5 HELIX 31 31 PRO B 309 SER B 314 5 6 HELIX 32 32 SER B 317 LEU B 325 1 9 SHEET 1 A 7 LYS A 49 HIS A 52 0 SHEET 2 A 7 MET A 28 THR A 35 1 N VAL A 33 O LEU A 51 SHEET 3 A 7 ILE A 4 VAL A 9 1 N ILE A 8 O PHE A 34 SHEET 4 A 7 VAL A 65 LEU A 68 1 O ILE A 67 N GLY A 7 SHEET 5 A 7 ASN A 88 ASP A 91 1 O ILE A 90 N LEU A 68 SHEET 6 A 7 VAL A 116 ILE A 118 1 O ILE A 118 N THR A 89 SHEET 7 A 7 GLY A 301 LYS A 303 1 O LYS A 303 N ALA A 117 SHEET 1 B 6 GLY A 142 TRP A 148 0 SHEET 2 B 6 HIS A 249 LYS A 258 -1 O PHE A 252 N PHE A 147 SHEET 3 B 6 LYS A 264 LEU A 273 -1 O PHE A 269 N VAL A 253 SHEET 4 B 6 LYS B 264 LEU B 273 -1 O SER B 270 N GLU A 268 SHEET 5 B 6 HIS B 249 LYS B 258 -1 N GLY B 257 O GLN B 265 SHEET 6 B 6 GLY B 142 TRP B 148 -1 N PHE B 147 O PHE B 252 SHEET 1 C 4 GLY A 151 VAL A 152 0 SHEET 2 C 4 VAL A 166 PRO A 175 -1 O THR A 173 N GLY A 151 SHEET 3 C 4 HIS A 197 LEU A 205 -1 O VAL A 204 N LYS A 167 SHEET 4 C 4 THR A 230 PHE A 234 1 O HIS A 233 N VAL A 203 SHEET 1 D 7 LYS B 49 HIS B 52 0 SHEET 2 D 7 MET B 28 THR B 35 1 N VAL B 33 O LEU B 51 SHEET 3 D 7 ILE B 4 VAL B 9 1 N ILE B 6 O GLU B 29 SHEET 4 D 7 VAL B 65 LEU B 68 1 O ILE B 67 N GLY B 7 SHEET 5 D 7 ASN B 88 ASP B 91 1 O ILE B 90 N LEU B 68 SHEET 6 D 7 VAL B 116 ILE B 118 1 O ILE B 118 N THR B 89 SHEET 7 D 7 GLY B 301 LYS B 303 1 O LYS B 303 N ALA B 117 SHEET 1 E 4 GLY B 151 VAL B 152 0 SHEET 2 E 4 VAL B 166 PRO B 175 -1 O THR B 173 N GLY B 151 SHEET 3 E 4 HIS B 197 LEU B 205 -1 O VAL B 204 N LYS B 167 SHEET 4 E 4 THR B 230 PHE B 234 1 O THR B 231 N CYS B 201 CISPEP 1 ASP A 124 PRO A 125 0 5.11 CISPEP 2 GLY A 149 LYS A 150 0 2.62 CISPEP 3 ASP B 124 PRO B 125 0 3.70 CISPEP 4 GLY B 149 LYS B 150 0 3.94 SITE 1 AC1 36 GLY A 10 TYR A 11 GLY A 12 ASN A 13 SITE 2 AC1 36 LEU A 14 THR A 35 ARG A 36 ARG A 37 SITE 3 AC1 36 CYS A 69 GLY A 70 GLY A 71 SER A 72 SITE 4 AC1 36 ASP A 75 SER A 92 ASP A 94 VAL A 121 SITE 5 AC1 36 TRP A 123 ASP A 124 PRO A 125 ASN A 276 SITE 6 AC1 36 THR A 280 NES A1002 HOH A1107 HOH A1113 SITE 7 AC1 36 HOH A1115 HOH A1120 HOH A1125 HOH A1137 SITE 8 AC1 36 HOH A1142 HOH A1147 HOH A1173 HOH A1204 SITE 9 AC1 36 HOH A1236 HOH A1272 HOH A1275 LYS B 213 SITE 1 AC2 12 TRP A 123 ASP A 124 TRP A 148 SER A 153 SITE 2 AC2 12 HIS A 156 THR A 173 ARG A 199 HIS A 249 SITE 3 AC2 12 NAP A1001 HOH A1139 HOH A1183 HOH A1239 SITE 1 AC3 6 VAL A 53 ASP A 54 GLU A 78 GLN A 79 SITE 2 AC3 6 TYR A 82 HOH A1228 SITE 1 AC4 35 LYS A 213 GLY B 10 TYR B 11 GLY B 12 SITE 2 AC4 35 ASN B 13 LEU B 14 THR B 35 ARG B 36 SITE 3 AC4 35 ARG B 37 CYS B 69 GLY B 70 GLY B 71 SITE 4 AC4 35 SER B 72 ASP B 75 SER B 92 ASP B 94 SITE 5 AC4 35 VAL B 121 TRP B 123 ASP B 124 PRO B 125 SITE 6 AC4 35 ASN B 276 THR B 280 NES B1002 HOH B1104 SITE 7 AC4 35 HOH B1112 HOH B1115 HOH B1121 HOH B1131 SITE 8 AC4 35 HOH B1133 HOH B1137 HOH B1225 HOH B1232 SITE 9 AC4 35 HOH B1234 HOH B1251 HOH B1252 SITE 1 AC5 11 TRP B 123 ASP B 124 TRP B 148 SER B 153 SITE 2 AC5 11 HIS B 156 THR B 173 ARG B 199 HIS B 249 SITE 3 AC5 11 NAP B1001 HOH B1147 HOH B1227 SITE 1 AC6 7 VAL B 53 ASP B 54 GLU B 78 GLN B 79 SITE 2 AC6 7 TYR B 82 PHE B 83 HOH B1207 CRYST1 123.021 123.021 193.302 90.00 90.00 120.00 H 3 18 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 0.008129 0.004693 0.000000 0.00000 SCALE2 0.000000 0.009386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005173 0.00000