HEADER OXIDOREDUCTASE 29-NOV-06 2O23 TITLE THE STRUCTURE OF WILD-TYPE HUMAN HADH2 (17BETA-HYDROXYSTEROID TITLE 2 DEHYDROGENASE TYPE 10) BOUND TO NAD+ AT 1.2 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HADH2 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HYDROXYACYL-COENZYME A DEHYDROGENASE, TYPE II; COMPND 5 EC: 1.1.1.178; 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 GENE: HADH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11-DERIVATIVE KEYWDS HSD17B10, SCHAD, ERAB, TYPE II HADH, 2-METHYL-3-HYDROXYBUTYRYL-COA KEYWDS 2 DEHYDROGENASE, MHBD, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, SGC, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.L.KAVANAGH,N.SHAFQAT,K.SCHOLER,J.DEBRECZENI,J.ZSCHOCKE,F.VON DELFT, AUTHOR 2 J.WEIGELT,C.ARROWSMITH,M.SUNDSTROM,A.EDWARDS,U.OPPERMANN,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 6 30-AUG-23 2O23 1 REMARK SEQADV REVDAT 5 31-JAN-18 2O23 1 AUTHOR JRNL REVDAT 4 18-OCT-17 2O23 1 REMARK REVDAT 3 13-JUL-11 2O23 1 VERSN REVDAT 2 24-FEB-09 2O23 1 VERSN REVDAT 1 12-DEC-06 2O23 0 JRNL AUTH K.L.KAVANAGH,N.SHAFQAT,K.SCHOLER,J.DEBRECZENI,J.ZSCHOCKE, JRNL AUTH 2 F.VON DELFT,J.WEIGELT,C.ARROWSMITH,M.SUNDSTROM,A.EDWARDS, JRNL AUTH 3 U.OPPERMANN JRNL TITL THE STRUCTURE OF WILD-TYPE HUMAN HADH2 JRNL TITL 2 (17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 10) BOUND TO NAD+ JRNL TITL 3 AT 1.2 A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 166548 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) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12109 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3582 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 614 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : 0.67000 REMARK 3 B12 (A**2) : -0.22000 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): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.030 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.028 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3917 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2567 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5372 ; 1.550 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6330 ; 0.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 552 ; 5.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;34.888 ;24.653 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 612 ;11.222 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;16.141 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 639 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4480 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 723 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 736 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2733 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1932 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1900 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 401 ; 0.161 ; 0.200 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): 8 ; 0.257 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 63 ; 0.215 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 54 ; 0.142 ; 0.200 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): 2784 ; 4.510 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1084 ; 2.796 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4119 ; 5.149 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1428 ; 7.416 ; 7.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1231 ; 8.854 ;11.000 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): 7038 ; 3.737 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 621 ;20.149 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6404 ; 7.413 ; 3.000 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 REMARK 4 REMARK 4 2O23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9687 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 168585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1U7T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.5% PEG 3350, 15% GLYCEROL, 0.17 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K, PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 46.05800 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 23.02900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.02900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.05800 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 843 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 882 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 903 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1068 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 880 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 980 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 CYS A 5 REMARK 465 LEU A 205 REMARK 465 LEU A 206 REMARK 465 THR A 207 REMARK 465 SER A 208 REMARK 465 LEU A 209 REMARK 465 PRO A 210 REMARK 465 GLU A 211 REMARK 465 LYS A 212 REMARK 465 VAL A 213 REMARK 465 CYS A 214 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 THR B 207 REMARK 465 SER B 208 REMARK 465 LEU B 209 REMARK 465 PRO B 210 REMARK 465 GLU B 211 REMARK 465 LYS B 212 REMARK 465 VAL B 213 REMARK 465 CYS B 214 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 6 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 44 CG OD1 ND2 REMARK 470 LYS A 52 CD CE NZ REMARK 470 LYS A 69 NZ REMARK 470 LYS A 105 CE NZ REMARK 470 GLN A 143 CG CD OE1 NE2 REMARK 470 ASN A 215 CG OD1 ND2 REMARK 470 PHE A 216 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 260 CD OE1 NE2 REMARK 470 SER A 263 OG REMARK 470 LYS B 69 CD CE NZ REMARK 470 LYS B 79 CE NZ REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 LYS B 105 CE NZ REMARK 470 ASN B 215 CG OD1 ND2 REMARK 470 GLN B 220 CG CD OE1 NE2 REMARK 470 SER B 263 OG 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 1028 O HOH B 997 2.17 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 ALA A 63 146.46 -170.60 REMARK 500 ALA A 154 -130.68 -94.97 REMARK 500 GLU A 160 55.20 -140.64 REMARK 500 ASP A 254 10.35 -157.40 REMARK 500 ALA B 63 145.58 -173.29 REMARK 500 LEU B 122 -60.30 -102.14 REMARK 500 ALA B 154 -131.00 -95.23 REMARK 500 ASP B 254 9.04 -155.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 130 0.08 SIDE CHAIN 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 NAD A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 801 DBREF 2O23 A 1 261 UNP Q6IBS9 Q6IBS9_HUMAN 1 261 DBREF 2O23 B 1 261 UNP Q6IBS9 Q6IBS9_HUMAN 1 261 SEQADV 2O23 GLY A -1 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 HIS A 0 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 GLY A 262 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 SER A 263 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 GLY B -1 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 HIS B 0 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 GLY B 262 UNP Q6IBS9 CLONING ARTIFACT SEQADV 2O23 SER B 263 UNP Q6IBS9 CLONING ARTIFACT SEQRES 1 A 265 GLY HIS MET ALA ALA ALA CYS ARG SER VAL LYS GLY LEU SEQRES 2 A 265 VAL ALA VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SEQRES 3 A 265 ALA THR ALA GLU ARG LEU VAL GLY GLN GLY ALA SER ALA SEQRES 4 A 265 VAL LEU LEU ASP LEU PRO ASN SER GLY GLY GLU ALA GLN SEQRES 5 A 265 ALA LYS LYS LEU GLY ASN ASN CYS VAL PHE ALA PRO ALA SEQRES 6 A 265 ASP VAL THR SER GLU LYS ASP VAL GLN THR ALA LEU ALA SEQRES 7 A 265 LEU ALA LYS GLY LYS PHE GLY ARG VAL ASP VAL ALA VAL SEQRES 8 A 265 ASN CYS ALA GLY ILE ALA VAL ALA SER LYS THR TYR ASN SEQRES 9 A 265 LEU LYS LYS GLY GLN THR HIS THR LEU GLU ASP PHE GLN SEQRES 10 A 265 ARG VAL LEU ASP VAL ASN LEU MET GLY THR PHE ASN VAL SEQRES 11 A 265 ILE ARG LEU VAL ALA GLY GLU MET GLY GLN ASN GLU PRO SEQRES 12 A 265 ASP GLN GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SEQRES 13 A 265 SER VAL ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA SEQRES 14 A 265 TYR SER ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU SEQRES 15 A 265 PRO ILE ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL SEQRES 16 A 265 MET THR ILE ALA PRO GLY LEU PHE GLY THR PRO LEU LEU SEQRES 17 A 265 THR SER LEU PRO GLU LYS VAL CYS ASN PHE LEU ALA SER SEQRES 18 A 265 GLN VAL PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU SEQRES 19 A 265 TYR ALA HIS LEU VAL GLN ALA ILE ILE GLU ASN PRO PHE SEQRES 20 A 265 LEU ASN GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG SEQRES 21 A 265 MET GLN PRO GLY SER SEQRES 1 B 265 GLY HIS MET ALA ALA ALA CYS ARG SER VAL LYS GLY LEU SEQRES 2 B 265 VAL ALA VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SEQRES 3 B 265 ALA THR ALA GLU ARG LEU VAL GLY GLN GLY ALA SER ALA SEQRES 4 B 265 VAL LEU LEU ASP LEU PRO ASN SER GLY GLY GLU ALA GLN SEQRES 5 B 265 ALA LYS LYS LEU GLY ASN ASN CYS VAL PHE ALA PRO ALA SEQRES 6 B 265 ASP VAL THR SER GLU LYS ASP VAL GLN THR ALA LEU ALA SEQRES 7 B 265 LEU ALA LYS GLY LYS PHE GLY ARG VAL ASP VAL ALA VAL SEQRES 8 B 265 ASN CYS ALA GLY ILE ALA VAL ALA SER LYS THR TYR ASN SEQRES 9 B 265 LEU LYS LYS GLY GLN THR HIS THR LEU GLU ASP PHE GLN SEQRES 10 B 265 ARG VAL LEU ASP VAL ASN LEU MET GLY THR PHE ASN VAL SEQRES 11 B 265 ILE ARG LEU VAL ALA GLY GLU MET GLY GLN ASN GLU PRO SEQRES 12 B 265 ASP GLN GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SEQRES 13 B 265 SER VAL ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA SEQRES 14 B 265 TYR SER ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU SEQRES 15 B 265 PRO ILE ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL SEQRES 16 B 265 MET THR ILE ALA PRO GLY LEU PHE GLY THR PRO LEU LEU SEQRES 17 B 265 THR SER LEU PRO GLU LYS VAL CYS ASN PHE LEU ALA SER SEQRES 18 B 265 GLN VAL PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU SEQRES 19 B 265 TYR ALA HIS LEU VAL GLN ALA ILE ILE GLU ASN PRO PHE SEQRES 20 B 265 LEU ASN GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG SEQRES 21 B 265 MET GLN PRO GLY SER HET NAD A 802 44 HET NAD B 803 44 HET GOL B 801 12 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *614(H2 O) HELIX 1 1 SER A 20 GLN A 33 1 14 HELIX 2 2 GLY A 46 GLY A 55 1 10 HELIX 3 3 SER A 67 GLY A 83 1 17 HELIX 4 4 THR A 110 LEU A 122 1 13 HELIX 5 5 LEU A 122 GLY A 137 1 16 HELIX 6 6 VAL A 156 GLY A 161 1 6 HELIX 7 7 GLN A 165 ALA A 187 1 23 HELIX 8 8 ASN A 215 GLN A 220 1 6 HELIX 9 9 ASP A 229 ASN A 243 1 15 HELIX 10 10 SER B 20 GLN B 33 1 14 HELIX 11 11 GLY B 46 GLY B 55 1 10 HELIX 12 12 SER B 67 GLY B 83 1 17 HELIX 13 13 THR B 110 LEU B 122 1 13 HELIX 14 14 LEU B 122 GLY B 137 1 16 HELIX 15 15 VAL B 156 GLY B 161 1 6 HELIX 16 16 GLN B 165 ALA B 187 1 23 HELIX 17 17 ASN B 215 GLN B 220 1 6 HELIX 18 18 ASP B 229 ASN B 243 1 15 SHEET 1 A 7 CYS A 58 PRO A 62 0 SHEET 2 A 7 SER A 36 ASP A 41 1 N LEU A 39 O ALA A 61 SHEET 3 A 7 VAL A 12 THR A 16 1 N ILE A 15 O VAL A 38 SHEET 4 A 7 VAL A 87 ASN A 90 1 O VAL A 89 N THR A 16 SHEET 5 A 7 GLY A 148 THR A 153 1 O ILE A 151 N ASN A 90 SHEET 6 A 7 ILE A 191 PRO A 198 1 O ARG A 192 N ILE A 150 SHEET 7 A 7 VAL A 250 LEU A 253 1 O ILE A 251 N ALA A 197 SHEET 1 B 2 TYR A 101 ASN A 102 0 SHEET 2 B 2 GLN A 107 THR A 108 -1 O GLN A 107 N ASN A 102 SHEET 1 C 7 CYS B 58 PRO B 62 0 SHEET 2 C 7 SER B 36 ASP B 41 1 N LEU B 39 O ALA B 61 SHEET 3 C 7 VAL B 12 THR B 16 1 N ILE B 15 O VAL B 38 SHEET 4 C 7 VAL B 87 ASN B 90 1 O VAL B 89 N VAL B 14 SHEET 5 C 7 GLY B 148 THR B 153 1 O ILE B 151 N ASN B 90 SHEET 6 C 7 ILE B 191 PRO B 198 1 O ILE B 196 N ASN B 152 SHEET 7 C 7 VAL B 250 LEU B 253 1 O ILE B 251 N ALA B 197 SHEET 1 D 2 TYR B 101 ASN B 102 0 SHEET 2 D 2 GLN B 107 THR B 108 -1 O GLN B 107 N ASN B 102 CISPEP 1 PHE A 223 PRO A 224 0 -4.86 CISPEP 2 PHE B 223 PRO B 224 0 -6.22 SITE 1 AC1 29 GLY A 17 SER A 20 GLY A 21 LEU A 22 SITE 2 AC1 29 ASP A 41 LEU A 42 ALA A 63 ASP A 64 SITE 3 AC1 29 VAL A 65 CYS A 91 ALA A 92 VAL A 120 SITE 4 AC1 29 THR A 153 ALA A 154 TYR A 168 LYS A 172 SITE 5 AC1 29 PRO A 198 GLY A 199 PHE A 201 THR A 203 SITE 6 AC1 29 PRO A 204 HOH A 806 HOH A 844 HOH A 851 SITE 7 AC1 29 HOH A 859 HOH A 928 HOH A 939 HOH A 964 SITE 8 AC1 29 HOH A 995 SITE 1 AC2 31 GLY B 17 SER B 20 GLY B 21 LEU B 22 SITE 2 AC2 31 ASP B 41 LEU B 42 ALA B 63 ASP B 64 SITE 3 AC2 31 VAL B 65 CYS B 91 ALA B 92 GLY B 93 SITE 4 AC2 31 VAL B 120 THR B 153 ALA B 154 TYR B 168 SITE 5 AC2 31 LYS B 172 PRO B 198 GLY B 199 LEU B 200 SITE 6 AC2 31 PHE B 201 THR B 203 PRO B 204 LEU B 205 SITE 7 AC2 31 HOH B 806 HOH B 845 HOH B 848 HOH B 867 SITE 8 AC2 31 HOH B 886 HOH B 913 HOH B1035 SITE 1 AC3 9 GLU A 249 VAL A 250 ARG A 252 GLU B 249 SITE 2 AC3 9 VAL B 250 ARG B 252 HOH B 884 HOH B 900 SITE 3 AC3 9 HOH B1090 CRYST1 117.037 117.037 69.087 90.00 90.00 120.00 P 32 2 1 12 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 0.008544 0.004933 0.000000 0.00000 SCALE2 0.000000 0.009866 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014475 0.00000