HEADER HYDROLASE/HYDROLASE INHIBITOR 20-JUN-22 8DEA TITLE SCAFFOLD HOPPING VIA RING OPENING ENABLES IDENTIFICATION OF ACYCLIC TITLE 2 COMPOUNDS AS NEW COMPLEMENT FACTOR D INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT FACTOR D; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: ADIPSIN,C3 CONVERTASE ACTIVATOR,PROPERDIN FACTOR D; COMPND 5 EC: 3.4.21.46; 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: CFD, DF, PFD; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 EXPRESSION_SYSTEM_CELL: EMBRYONIC KIDNEY KEYWDS SERINE PROTEASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.RAMAN,Y.S.BABU REVDAT 3 23-OCT-24 8DEA 1 REMARK REVDAT 2 18-OCT-23 8DEA 1 REMARK REVDAT 1 02-NOV-22 8DEA 0 JRNL AUTH W.ZHANG,M.WU,S.VADLAKONDA,L.JUAREZ,X.CHENG,S.MUPPA, JRNL AUTH 2 V.CHINTAREDDY,L.VOGETI,D.KELLOGG-YELDER,J.WILLIAMS,K.POLACH, JRNL AUTH 3 X.CHEN,K.RAMAN,Y.S.BABU,P.KOTIAN JRNL TITL SCAFFOLD HOPPING VIA RING OPENING ENABLES IDENTIFICATION OF JRNL TITL 2 ACYCLIC COMPOUNDS AS NEW COMPLEMENT FACTOR D INHIBITORS. JRNL REF BIOORG.MED.CHEM. V. 74 17034 2022 JRNL REFN ESSN 1464-3391 JRNL PMID 36272185 JRNL DOI 10.1016/J.BMC.2022.117034 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0350 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 34591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.897 REMARK 3 FREE R VALUE TEST SET COUNT : 1694 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) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1410 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04800 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.01100 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): 0.557 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.321 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.238 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.716 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6750 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6216 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9186 ; 1.372 ; 1.654 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14472 ; 0.533 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 856 ; 7.637 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;19.685 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1052 ;16.172 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1034 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7772 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1248 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1159 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 124 ; 0.229 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3125 ; 0.163 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 161 ; 0.153 ; 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): 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): 3456 ; 2.762 ; 3.345 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3456 ; 2.762 ; 3.345 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4296 ; 4.260 ; 4.990 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4297 ; 4.261 ; 4.993 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3294 ; 2.756 ; 3.604 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3295 ; 2.756 ; 3.604 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4890 ; 4.219 ; 5.285 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4891 ; 4.219 ; 5.285 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8DEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 170 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36438 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1DIC REMARK 200 REMARK 200 REMARK: SQUARE BLOCKS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4K 25% , 0.1M MES 5.8 BUFFER, PH REMARK 280 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-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 36.51600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 120.43200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.51600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 120.43200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 ASP A 45 REMARK 465 ALA A 46 REMARK 465 ALA A 47 REMARK 465 ASP A 48 REMARK 465 ARG A 156 REMARK 465 ARG A 157 REMARK 465 THR A 158 REMARK 465 HIS A 159 REMARK 465 HIS A 160 REMARK 465 ASP A 161 REMARK 465 GLY A 162 REMARK 465 ALA A 163 REMARK 465 ILE A 164 REMARK 465 ASP B 45 REMARK 465 ALA B 46 REMARK 465 ALA B 47 REMARK 465 ASP B 48 REMARK 465 ARG B 156 REMARK 465 ARG B 157 REMARK 465 THR B 158 REMARK 465 HIS B 159 REMARK 465 HIS B 160 REMARK 465 ASP B 161 REMARK 465 GLY B 162 REMARK 465 ALA B 163 REMARK 465 ILE B 164 REMARK 465 ASP C 45 REMARK 465 ALA C 46 REMARK 465 ALA C 47 REMARK 465 ASP C 48 REMARK 465 ARG C 156 REMARK 465 ARG C 157 REMARK 465 THR C 158 REMARK 465 HIS C 159 REMARK 465 HIS C 160 REMARK 465 ASP C 161 REMARK 465 GLY C 162 REMARK 465 ALA C 163 REMARK 465 ILE C 164 REMARK 465 ASP D 45 REMARK 465 ALA D 46 REMARK 465 ALA D 47 REMARK 465 ASP D 48 REMARK 465 ARG D 156 REMARK 465 ARG D 157 REMARK 465 THR D 158 REMARK 465 HIS D 159 REMARK 465 HIS D 160 REMARK 465 ASP D 161 REMARK 465 GLY D 162 REMARK 465 ALA D 163 REMARK 465 ILE D 164 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 ASN A 174 O REMARK 470 ASN B 174 O REMARK 470 ASN C 174 O REMARK 470 ASN D 174 O 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 B 424 O HOH B 427 2.11 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 ARG A 12 75.20 -118.11 REMARK 500 SER A 38 -158.34 -139.97 REMARK 500 CYS A 42 14.01 -63.22 REMARK 500 ASP A 89 54.42 -92.50 REMARK 500 ARG A 175 -64.97 81.34 REMARK 500 LYS A 180 121.04 -29.88 REMARK 500 HIS B 10 -0.89 80.82 REMARK 500 ARG B 12 77.80 -109.38 REMARK 500 SER B 38 -152.28 -141.03 REMARK 500 ARG B 68 118.43 -160.62 REMARK 500 ARG B 175 -57.52 79.01 REMARK 500 ASP C 89 52.53 -90.70 REMARK 500 ASP C 114 71.37 -69.31 REMARK 500 ARG C 175 -69.31 77.05 REMARK 500 SER C 183 132.82 -35.90 REMARK 500 SER C 229 -74.59 -84.24 REMARK 500 ASN D 21 -126.22 60.25 REMARK 500 SER D 38 -156.29 -138.03 REMARK 500 LEU D 43 -20.19 -151.11 REMARK 500 LEU D 73 -100.01 -79.19 REMARK 500 ARG D 175 -54.78 79.85 REMARK 500 SER D 201 143.37 -39.35 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 A 5 0.09 SIDE CHAIN REMARK 500 ARG A 112 0.14 SIDE CHAIN REMARK 500 ARG A 136 0.08 SIDE CHAIN REMARK 500 ARG A 151 0.09 SIDE CHAIN REMARK 500 ARG A 167 0.10 SIDE CHAIN REMARK 500 ARG A 175 0.09 SIDE CHAIN REMARK 500 ARG A 215 0.08 SIDE CHAIN REMARK 500 ARG B 5 0.17 SIDE CHAIN REMARK 500 ARG B 215 0.10 SIDE CHAIN REMARK 500 ARG C 115 0.08 SIDE CHAIN REMARK 500 ARG C 136 0.11 SIDE CHAIN REMARK 500 ARG C 151 0.14 SIDE CHAIN REMARK 500 ARG C 167 0.10 SIDE CHAIN REMARK 500 ARG D 5 0.26 SIDE CHAIN REMARK 500 ARG D 12 0.08 SIDE CHAIN REMARK 500 ARG D 106 0.10 SIDE CHAIN REMARK 500 ARG D 112 0.18 SIDE CHAIN REMARK 500 ARG D 115 0.15 SIDE CHAIN REMARK 500 ARG D 136 0.24 SIDE CHAIN REMARK 500 ARG D 167 0.23 SIDE CHAIN REMARK 500 ARG D 176 0.18 SIDE CHAIN REMARK 500 ARG D 207 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DIC RELATED DB: PDB REMARK 900 FACTORD REMARK 900 RELATED ID: 1BFP RELATED DB: PDB REMARK 900 FACTORD DBREF 8DEA A 1 228 UNP P00746 CFAD_HUMAN 26 253 DBREF 8DEA B 1 228 UNP P00746 CFAD_HUMAN 26 253 DBREF 8DEA C 1 228 UNP P00746 CFAD_HUMAN 26 253 DBREF 8DEA D 1 228 UNP P00746 CFAD_HUMAN 26 253 SEQADV 8DEA SER A 229 UNP P00746 EXPRESSION TAG SEQADV 8DEA ALA A 230 UNP P00746 EXPRESSION TAG SEQADV 8DEA SER B 229 UNP P00746 EXPRESSION TAG SEQADV 8DEA ALA B 230 UNP P00746 EXPRESSION TAG SEQADV 8DEA SER C 229 UNP P00746 EXPRESSION TAG SEQADV 8DEA ALA C 230 UNP P00746 EXPRESSION TAG SEQADV 8DEA SER D 229 UNP P00746 EXPRESSION TAG SEQADV 8DEA ALA D 230 UNP P00746 EXPRESSION TAG SEQRES 1 A 230 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 A 230 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 A 230 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 A 230 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 A 230 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 A 230 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 A 230 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 A 230 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 A 230 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 A 230 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 A 230 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 A 230 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 A 230 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 A 230 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 A 230 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 A 230 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 A 230 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 A 230 TRP ILE ASP SER VAL LEU ALA SER ALA SEQRES 1 B 230 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 B 230 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 B 230 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 B 230 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 B 230 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 B 230 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 B 230 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 B 230 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 B 230 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 B 230 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 B 230 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 B 230 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 B 230 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 B 230 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 B 230 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 B 230 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 B 230 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 B 230 TRP ILE ASP SER VAL LEU ALA SER ALA SEQRES 1 C 230 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 C 230 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 C 230 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 C 230 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 C 230 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 C 230 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 C 230 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 C 230 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 C 230 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 C 230 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 C 230 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 C 230 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 C 230 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 C 230 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 C 230 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 C 230 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 C 230 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 C 230 TRP ILE ASP SER VAL LEU ALA SER ALA SEQRES 1 D 230 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 D 230 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 D 230 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 D 230 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 D 230 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 D 230 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 D 230 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 D 230 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 D 230 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 D 230 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 D 230 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 D 230 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 D 230 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 D 230 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 D 230 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 D 230 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 D 230 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 D 230 TRP ILE ASP SER VAL LEU ALA SER ALA HET R7X A 301 27 HET R7X B 301 27 HET R7X C 301 27 HET GOL C 302 6 HET GOL C 303 6 HET R7X D 301 27 HETNAM R7X 1-[(3-ACETYLPHENYL)ACETYL]-N-(6-BROMOPYRIDIN-2-YL)-L- HETNAM 2 R7X PROLINAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 R7X 4(C20 H20 BR N3 O3) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 11 HOH *84(H2 O) HELIX 1 AA1 ALA A 39 LEU A 43 5 5 HELIX 2 AA2 ASP A 150 ASN A 155 1 6 HELIX 3 AA3 TYR A 219 SER A 229 1 11 HELIX 4 AA4 ALA B 39 GLU B 44 1 6 HELIX 5 AA5 ASP B 150 ASN B 155 1 6 HELIX 6 AA6 TYR B 219 ALA B 228 1 10 HELIX 7 AA7 ASP C 150 ASN C 155 1 6 HELIX 8 AA8 TYR C 219 LEU C 227 1 9 HELIX 9 AA9 ASP D 150 ASN D 155 1 6 HELIX 10 AB1 TYR D 219 ALA D 228 1 10 SHEET 1 AA1 8 ARG A 5 GLU A 6 0 SHEET 2 AA1 8 GLN A 142 LEU A 149 -1 O HIS A 143 N ARG A 5 SHEET 3 AA1 8 LEU A 168 ALA A 171 -1 O CYS A 170 N LEU A 149 SHEET 4 AA1 8 GLY A 211 ARG A 215 -1 O TYR A 213 N MET A 169 SHEET 5 AA1 8 VAL A 192 VAL A 197 -1 N VAL A 196 O THR A 214 SHEET 6 AA1 8 PRO A 186 CYS A 189 -1 N LEU A 187 O GLY A 195 SHEET 7 AA1 8 LEU A 122 GLY A 127 -1 N ASP A 124 O VAL A 188 SHEET 8 AA1 8 GLN A 142 LEU A 149 -1 O LEU A 146 N CYS A 123 SHEET 1 AA2 7 MET A 15 LEU A 20 0 SHEET 2 AA2 7 ALA A 23 ALA A 32 -1 O CYS A 26 N VAL A 18 SHEET 3 AA2 7 TRP A 35 SER A 38 -1 O LEU A 37 N VAL A 29 SHEET 4 AA2 7 LEU A 91 LEU A 95 -1 O LEU A 91 N SER A 38 SHEET 5 AA2 7 ARG A 68 PRO A 77 -1 N LEU A 73 O GLN A 94 SHEET 6 AA2 7 VAL A 51 LEU A 55 -1 N LEU A 55 O ARG A 68 SHEET 7 AA2 7 MET A 15 LEU A 20 -1 N GLN A 19 O GLN A 52 SHEET 1 AA3 7 ARG B 5 GLU B 6 0 SHEET 2 AA3 7 GLN B 142 PRO B 147 -1 O HIS B 143 N ARG B 5 SHEET 3 AA3 7 LEU B 122 GLY B 127 -1 N CYS B 123 O LEU B 146 SHEET 4 AA3 7 PRO B 186 CYS B 189 -1 O VAL B 188 N ASP B 124 SHEET 5 AA3 7 VAL B 192 VAL B 197 -1 O GLU B 194 N LEU B 187 SHEET 6 AA3 7 GLY B 211 ARG B 215 -1 O THR B 214 N VAL B 196 SHEET 7 AA3 7 LEU B 168 ALA B 171 -1 N MET B 169 O TYR B 213 SHEET 1 AA4 7 MET B 15 LEU B 20 0 SHEET 2 AA4 7 HIS B 24 ALA B 32 -1 O CYS B 26 N VAL B 18 SHEET 3 AA4 7 TRP B 35 SER B 38 -1 O LEU B 37 N VAL B 29 SHEET 4 AA4 7 LEU B 91 LEU B 95 -1 O LEU B 91 N SER B 38 SHEET 5 AA4 7 ARG B 68 PRO B 77 -1 N LEU B 73 O GLN B 94 SHEET 6 AA4 7 VAL B 51 LEU B 55 -1 N VAL B 53 O TYR B 70 SHEET 7 AA4 7 MET B 15 LEU B 20 -1 N SER B 17 O LEU B 54 SHEET 1 AA5 8 ARG C 5 GLU C 6 0 SHEET 2 AA5 8 GLN C 142 LEU C 149 -1 O HIS C 143 N ARG C 5 SHEET 3 AA5 8 LEU C 168 ALA C 171 -1 O CYS C 170 N LEU C 149 SHEET 4 AA5 8 GLY C 211 ARG C 215 -1 O TYR C 213 N MET C 169 SHEET 5 AA5 8 VAL C 192 VAL C 197 -1 N VAL C 196 O THR C 214 SHEET 6 AA5 8 PRO C 186 CYS C 189 -1 N LEU C 187 O GLU C 194 SHEET 7 AA5 8 LEU C 122 GLY C 127 -1 N ASP C 124 O VAL C 188 SHEET 8 AA5 8 GLN C 142 LEU C 149 -1 O LEU C 146 N CYS C 123 SHEET 1 AA6 7 MET C 15 LEU C 20 0 SHEET 2 AA6 7 ALA C 23 ALA C 32 -1 O CYS C 26 N VAL C 18 SHEET 3 AA6 7 TRP C 35 SER C 38 -1 O LEU C 37 N VAL C 29 SHEET 4 AA6 7 LEU C 91 LEU C 95 -1 O LEU C 91 N SER C 38 SHEET 5 AA6 7 ARG C 68 PRO C 77 -1 N VAL C 76 O LEU C 92 SHEET 6 AA6 7 VAL C 51 LEU C 55 -1 N VAL C 53 O TYR C 70 SHEET 7 AA6 7 MET C 15 LEU C 20 -1 N GLN C 19 O GLN C 52 SHEET 1 AA7 8 ARG D 5 GLU D 6 0 SHEET 2 AA7 8 GLN D 142 LEU D 149 -1 O HIS D 143 N ARG D 5 SHEET 3 AA7 8 LEU D 168 ALA D 171 -1 O CYS D 170 N LEU D 149 SHEET 4 AA7 8 GLY D 211 ARG D 215 -1 O TYR D 213 N MET D 169 SHEET 5 AA7 8 VAL D 192 VAL D 197 -1 N VAL D 196 O THR D 214 SHEET 6 AA7 8 PRO D 186 CYS D 189 -1 N LEU D 187 O GLU D 194 SHEET 7 AA7 8 LEU D 122 GLY D 127 -1 N ASP D 124 O VAL D 188 SHEET 8 AA7 8 GLN D 142 LEU D 149 -1 O GLN D 142 N GLY D 127 SHEET 1 AA8 7 MET D 15 LEU D 20 0 SHEET 2 AA8 7 ALA D 23 ALA D 32 -1 O CYS D 26 N VAL D 18 SHEET 3 AA8 7 TRP D 35 SER D 38 -1 O LEU D 37 N VAL D 29 SHEET 4 AA8 7 LEU D 91 LEU D 95 -1 O LEU D 91 N SER D 38 SHEET 5 AA8 7 ARG D 68 PRO D 77 -1 N ARG D 74 O GLN D 94 SHEET 6 AA8 7 VAL D 51 LEU D 55 -1 N VAL D 53 O TYR D 70 SHEET 7 AA8 7 MET D 15 LEU D 20 -1 N GLN D 19 O GLN D 52 SSBOND 1 CYS A 26 CYS A 42 1555 1555 2.05 SSBOND 2 CYS A 123 CYS A 189 1555 1555 2.00 SSBOND 3 CYS A 154 CYS A 170 1555 1555 2.05 SSBOND 4 CYS A 179 CYS A 204 1555 1555 2.04 SSBOND 5 CYS B 26 CYS B 42 1555 1555 1.99 SSBOND 6 CYS B 123 CYS B 189 1555 1555 2.03 SSBOND 7 CYS B 154 CYS B 170 1555 1555 2.02 SSBOND 8 CYS B 179 CYS B 204 1555 1555 2.08 SSBOND 9 CYS C 26 CYS C 42 1555 1555 2.05 SSBOND 10 CYS C 123 CYS C 189 1555 1555 2.06 SSBOND 11 CYS C 154 CYS C 170 1555 1555 2.03 SSBOND 12 CYS C 179 CYS C 204 1555 1555 2.06 SSBOND 13 CYS D 26 CYS D 42 1555 1555 2.03 SSBOND 14 CYS D 123 CYS D 189 1555 1555 2.04 SSBOND 15 CYS D 154 CYS D 170 1555 1555 2.02 SSBOND 16 CYS D 179 CYS D 204 1555 1555 2.09 CRYST1 44.898 73.032 240.864 90.00 90.00 90.00 P 2 21 21 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 0.022273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013693 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004152 0.00000