PDB Short entry for 2GVJ HEADER TRANSFERASE 02-MAY-06 2GVJ TITLE CRYSTAL STRUCTURE OF HUMAN NMPRTASE IN COMPLEX WITH FK866 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NAMPRTASE, NAMPT, PRE-B CELL-ENHANCING FACTOR, PRE-B-CELL COMPND 5 COLONY-ENHANCING FACTOR 1, VISFATIN; COMPND 6 EC: 2.4.2.12; COMPND 7 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: NAMPT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NMPRTASE, VISFATIN, PBEF, CANCER, FK866, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.KHAN,X.TAO,L.TONG REVDAT 4 09-NOV-16 2GVJ 1 FORMUL HETNAM VERSN REVDAT 3 24-FEB-09 2GVJ 1 VERSN REVDAT 2 18-JUL-06 2GVJ 1 JRNL REVDAT 1 20-JUN-06 2GVJ 0 JRNL AUTH J.A.KHAN,X.TAO,L.TONG JRNL TITL MOLECULAR BASIS FOR THE INHIBITION OF HUMAN NMPRTASE, A JRNL TITL 2 NOVEL TARGET FOR ANTICANCER AGENTS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 582 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16783377 JRNL DOI 10.1038/NSMB1105 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 57137 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3024 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3652 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 205 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7431 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 775 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : -0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.312 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.244 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.179 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.600 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.897 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.854 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7669 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10388 ; 1.204 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 925 ; 6.079 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 347 ;39.320 ;24.870 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1330 ;15.195 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.265 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1135 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5776 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4086 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5204 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 822 ; 0.173 ; 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): 60 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.217 ; 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): 4749 ; 0.466 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7474 ; 0.744 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3418 ; 1.147 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2914 ; 1.733 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 9 A 41 4 REMARK 3 1 B 9 B 41 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 283 ; 0.41 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 283 ; 0.40 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 54 A 484 4 REMARK 3 1 B 54 B 484 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 3420 ; 0.34 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 3420 ; 0.36 ; 2.00 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 2GVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-06. REMARK 100 THE RCSB ID CODE IS RCSB037599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57137 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 82.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: COMO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 3350, 200 MM NACL, BACL2 AS REMARK 280 ADDITIVE, PH 9.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 52.94800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 10460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 MSE A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 LYS A 42 REMARK 465 LYS A 43 REMARK 465 THR A 44 REMARK 465 GLU A 45 REMARK 465 ASN A 46 REMARK 465 SER A 47 REMARK 465 LYS A 48 REMARK 465 LEU A 49 REMARK 465 ARG A 50 REMARK 465 LYS A 51 REMARK 465 VAL A 52 REMARK 465 LYS A 53 REMARK 465 LEU A 486 REMARK 465 GLU A 487 REMARK 465 ALA A 488 REMARK 465 ALA A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 MSE B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 ALA B 4 REMARK 465 ALA B 5 REMARK 465 GLU B 6 REMARK 465 ALA B 7 REMARK 465 GLU B 8 REMARK 465 LYS B 42 REMARK 465 LYS B 43 REMARK 465 THR B 44 REMARK 465 GLU B 45 REMARK 465 ASN B 46 REMARK 465 SER B 47 REMARK 465 LYS B 48 REMARK 465 LEU B 49 REMARK 465 ARG B 50 REMARK 465 LYS B 51 REMARK 465 VAL B 52 REMARK 465 LYS B 53 REMARK 465 GLU B 485 REMARK 465 LEU B 486 REMARK 465 GLU B 487 REMARK 465 ALA B 488 REMARK 465 ALA B 489 REMARK 465 HIS B 490 REMARK 465 HIS B 491 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 1327 O HOH B 1219 2.09 REMARK 500 O HOH B 642 O HOH B 942 2.11 REMARK 500 O HOH A 1046 O HOH B 1300 2.16 REMARK 500 NH1 ARG A 302 O HOH A 1448 2.17 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 ASP A 138 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 456 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 138 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 474 CB - CG - OD2 ANGL. DEV. = 5.5 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 29 33.86 72.54 REMARK 500 PHE A 96 128.52 175.48 REMARK 500 CYS A 141 34.73 -96.21 REMARK 500 GLU A 187 4.54 -67.11 REMARK 500 TYR A 231 -58.17 -128.90 REMARK 500 GLU A 293 -65.95 -126.65 REMARK 500 ASP A 313 17.98 -148.73 REMARK 500 ASN A 337 107.80 63.76 REMARK 500 LYS A 389 48.24 -81.65 REMARK 500 ASP A 416 69.99 -157.27 REMARK 500 ASP A 420 84.22 -153.31 REMARK 500 TYR A 453 -161.51 -104.06 REMARK 500 ILE A 484 101.60 -16.11 REMARK 500 GLN B 154 -9.49 -56.35 REMARK 500 ASN B 182 -164.80 -160.90 REMARK 500 VAL B 221 47.91 -82.85 REMARK 500 TYR B 231 -52.27 -129.18 REMARK 500 TYR B 281 -50.24 -129.48 REMARK 500 GLU B 293 -61.68 -130.04 REMARK 500 ASP B 313 20.20 -148.85 REMARK 500 ASP B 416 70.33 -157.71 REMARK 500 ASP B 420 87.33 -152.78 REMARK 500 GLU B 451 24.34 -78.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 337 SER A 338 133.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1394 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH B1125 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH B1349 DISTANCE = 8.10 ANGSTROMS REMARK 525 HOH B1353 DISTANCE = 5.32 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGB B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGB A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GVG RELATED DB: PDB DBREF 2GVJ A 1 491 UNP P43490 NAMPT_HUMAN 1 491 DBREF 2GVJ B 1 491 UNP P43490 NAMPT_HUMAN 1 491 SEQADV 2GVJ MSE A 1 UNP P43490 MET 1 MODIFIED RESIDUE SEQADV 2GVJ MSE A 368 UNP P43490 MET 368 MODIFIED RESIDUE SEQADV 2GVJ MSE A 372 UNP P43490 MET 372 MODIFIED RESIDUE SEQADV 2GVJ MSE B 1 UNP P43490 MET 1 MODIFIED RESIDUE SEQADV 2GVJ MSE B 368 UNP P43490 MET 368 MODIFIED RESIDUE SEQADV 2GVJ MSE B 372 UNP P43490 MET 372 MODIFIED RESIDUE SEQRES 1 A 491 MSE ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 A 491 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 A 491 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 A 491 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 A 491 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 A 491 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 A 491 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 A 491 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 A 491 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 A 491 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 A 491 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 A 491 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 A 491 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 A 491 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 A 491 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 A 491 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 A 491 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 A 491 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 A 491 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 A 491 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 A 491 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 A 491 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 A 491 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 A 491 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 A 491 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 A 491 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 A 491 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 A 491 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 A 491 VAL GLU GLY MSE LYS GLN LYS MSE TRP SER ILE GLU ASN SEQRES 30 A 491 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 A 491 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 A 491 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 A 491 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 A 491 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 A 491 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 A 491 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 A 491 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 A 491 LEU ASN ILE GLU LEU GLU ALA ALA HIS HIS SEQRES 1 B 491 MSE ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 B 491 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 B 491 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 B 491 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 B 491 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 B 491 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 B 491 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 B 491 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 B 491 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 B 491 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 B 491 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 B 491 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 B 491 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 B 491 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 B 491 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 B 491 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 B 491 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 B 491 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 B 491 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 B 491 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 B 491 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 B 491 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 B 491 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 B 491 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 B 491 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 B 491 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 B 491 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 B 491 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 B 491 VAL GLU GLY MSE LYS GLN LYS MSE TRP SER ILE GLU ASN SEQRES 30 B 491 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 B 491 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 B 491 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 B 491 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 B 491 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 B 491 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 B 491 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 B 491 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 B 491 LEU ASN ILE GLU LEU GLU ALA ALA HIS HIS MODRES 2GVJ MSE A 368 MET SELENOMETHIONINE MODRES 2GVJ MSE A 372 MET SELENOMETHIONINE MODRES 2GVJ MSE B 368 MET SELENOMETHIONINE MODRES 2GVJ MSE B 372 MET SELENOMETHIONINE HET MSE A 368 8 HET MSE A 372 8 HET MSE B 368 8 HET MSE B 372 8 HET DGB B 501 29 HET DGB A 502 29 HETNAM MSE SELENOMETHIONINE HETNAM DGB (2E)-N-{4-[1-(BENZENECARBONYL)PIPERIDIN-4-YL]BUTYL}-3- HETNAM 2 DGB (PYRIDIN-3-YL)PROP-2-ENAMIDE HETSYN DGB FK-866 FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 DGB 2(C24 H29 N3 O2) FORMUL 5 HOH *775(H2 O) HELIX 1 1 ASN A 10 ALA A 14 5 5 HELIX 2 2 ASP A 16 GLN A 25 5 10 HELIX 3 3 GLY A 61 LEU A 70 1 10 HELIX 4 4 THR A 76 GLN A 92 1 17 HELIX 5 5 ASN A 97 ASP A 109 1 13 HELIX 6 6 ASP A 138 TYR A 142 5 5 HELIX 7 7 TRP A 143 ILE A 148 1 6 HELIX 8 8 ILE A 148 GLN A 154 1 7 HELIX 9 9 SER A 155 GLY A 181 1 27 HELIX 10 10 GLY A 185 TYR A 188 5 4 HELIX 11 11 SER A 200 LEU A 212 1 13 HELIX 12 12 VAL A 221 TYR A 231 1 11 HELIX 13 13 GLU A 246 ALA A 252 1 7 HELIX 14 14 TRP A 253 ASP A 256 5 4 HELIX 15 15 HIS A 257 PHE A 269 1 13 HELIX 16 16 ASP A 282 LYS A 289 1 8 HELIX 17 17 LEU A 295 VAL A 300 1 6 HELIX 18 18 ASN A 316 PHE A 332 1 17 HELIX 19 19 ASP A 357 LYS A 371 1 15 HELIX 20 20 SER A 374 GLU A 376 5 3 HELIX 21 21 GLY A 383 GLN A 388 1 6 HELIX 22 22 ASP A 420 ARG A 424 5 5 HELIX 23 23 GLY A 446 LEU A 450 5 5 HELIX 24 24 SER A 472 ALA A 480 1 9 HELIX 25 25 ASN B 10 ALA B 14 5 5 HELIX 26 26 ASP B 16 GLN B 25 5 10 HELIX 27 27 GLY B 61 LEU B 70 1 10 HELIX 28 28 THR B 76 PHE B 91 1 16 HELIX 29 29 ASN B 97 ASP B 109 1 13 HELIX 30 30 ASP B 138 TYR B 142 5 5 HELIX 31 31 TRP B 143 ILE B 148 1 6 HELIX 32 32 ILE B 148 GLN B 154 1 7 HELIX 33 33 SER B 155 SER B 180 1 26 HELIX 34 34 GLY B 185 TYR B 188 5 4 HELIX 35 35 GLY B 194 VAL B 198 5 5 HELIX 36 36 SER B 200 LEU B 212 1 13 HELIX 37 37 ALA B 222 TYR B 231 1 10 HELIX 38 38 GLU B 246 ALA B 252 1 7 HELIX 39 39 TRP B 253 ASP B 256 5 4 HELIX 40 40 HIS B 257 PHE B 269 1 13 HELIX 41 41 ASP B 282 LYS B 289 1 8 HELIX 42 42 LEU B 295 VAL B 300 1 6 HELIX 43 43 ASN B 316 LYS B 330 1 15 HELIX 44 44 ASP B 357 LYS B 371 1 15 HELIX 45 45 SER B 374 GLU B 376 5 3 HELIX 46 46 GLY B 383 GLN B 388 1 6 HELIX 47 47 ASP B 420 ARG B 424 5 5 HELIX 48 48 GLY B 446 GLY B 454 5 9 HELIX 49 49 SER B 472 ALA B 480 1 9 SHEET 1 A 7 LEU A 409 ASN A 412 0 SHEET 2 A 7 CYS A 397 THR A 406 -1 N THR A 406 O LEU A 409 SHEET 3 A 7 THR A 30 CYS A 39 -1 N TYR A 34 O TYR A 403 SHEET 4 A 7 VAL A 130 ASN A 136 -1 O VAL A 134 N SER A 35 SHEET 5 A 7 ILE A 114 ALA A 118 -1 N GLU A 115 O GLU A 135 SHEET 6 A 7 HIS A 459 LYS A 463 -1 O PHE A 462 N ILE A 116 SHEET 7 A 7 LYS A 466 VAL A 467 -1 O LYS A 466 N LYS A 463 SHEET 1 B 2 GLU A 56 VAL A 58 0 SHEET 2 B 2 VAL A 124 PRO A 126 -1 O ILE A 125 N THR A 57 SHEET 1 C 5 LEU A 190 ASP A 192 0 SHEET 2 C 5 ILE A 378 SER A 382 1 O PHE A 380 N HIS A 191 SHEET 3 C 5 LEU A 348 GLN A 352 1 N GLN A 352 O GLY A 381 SHEET 4 C 5 LEU A 308 ARG A 311 1 N LEU A 308 O ARG A 349 SHEET 5 C 5 VAL A 274 VAL A 277 1 N VAL A 274 O ILE A 309 SHEET 1 D 2 THR A 335 GLU A 336 0 SHEET 2 D 2 LYS A 342 LEU A 343 -1 O LEU A 343 N THR A 335 SHEET 1 E 2 SER A 431 ARG A 434 0 SHEET 2 E 2 PHE A 440 LEU A 443 -1 O VAL A 441 N HIS A 433 SHEET 1 F 7 LEU B 409 ASN B 412 0 SHEET 2 F 7 CYS B 397 THR B 406 -1 N VAL B 404 O ILE B 411 SHEET 3 F 7 THR B 30 CYS B 39 -1 N TYR B 34 O TYR B 403 SHEET 4 F 7 VAL B 130 ASN B 136 -1 O VAL B 134 N SER B 35 SHEET 5 F 7 ILE B 114 ALA B 118 -1 N GLU B 115 O GLU B 135 SHEET 6 F 7 HIS B 459 LYS B 463 -1 O PHE B 462 N ILE B 116 SHEET 7 F 7 LYS B 466 VAL B 467 -1 O LYS B 466 N LYS B 463 SHEET 1 G 2 GLU B 56 VAL B 58 0 SHEET 2 G 2 VAL B 124 PRO B 126 -1 O ILE B 125 N THR B 57 SHEET 1 H 5 LEU B 190 ASP B 192 0 SHEET 2 H 5 ILE B 378 SER B 382 1 O PHE B 380 N HIS B 191 SHEET 3 H 5 LEU B 348 GLN B 352 1 N GLN B 352 O ALA B 379 SHEET 4 H 5 LEU B 308 ARG B 311 1 N LEU B 308 O ARG B 349 SHEET 5 H 5 VAL B 274 VAL B 277 1 N VAL B 274 O ILE B 309 SHEET 1 I 2 THR B 335 GLU B 336 0 SHEET 2 I 2 LYS B 342 LEU B 343 -1 O LEU B 343 N THR B 335 SHEET 1 J 2 SER B 431 ARG B 434 0 SHEET 2 J 2 PHE B 440 LEU B 443 -1 O VAL B 441 N HIS B 433 LINK C GLY A 367 N MSE A 368 1555 1555 1.34 LINK C MSE A 368 N LYS A 369 1555 1555 1.33 LINK C LYS A 371 N MSE A 372 1555 1555 1.33 LINK C MSE A 372 N TRP A 373 1555 1555 1.33 LINK C GLY B 367 N MSE B 368 1555 1555 1.33 LINK C MSE B 368 N LYS B 369 1555 1555 1.33 LINK C LYS B 371 N MSE B 372 1555 1555 1.33 LINK C MSE B 372 N TRP B 373 1555 1555 1.33 SITE 1 AC1 16 TYR A 18 LYS B 189 PHE B 193 ARG B 196 SITE 2 AC1 16 ASP B 219 VAL B 242 ALA B 244 SER B 275 SITE 3 AC1 16 PRO B 307 ARG B 311 ARG B 349 VAL B 350 SITE 4 AC1 16 GLU B 376 ILE B 378 ALA B 379 HOH B 635 SITE 1 AC2 18 LYS A 189 HIS A 191 PHE A 193 ARG A 196 SITE 2 AC2 18 ASP A 219 VAL A 242 ALA A 244 SER A 275 SITE 3 AC2 18 PRO A 307 ARG A 311 ARG A 349 VAL A 350 SITE 4 AC2 18 GLU A 376 ILE A 378 ALA A 379 HOH A 645 SITE 5 AC2 18 HOH A1339 TYR B 18 CRYST1 60.780 105.896 83.427 90.00 96.45 90.00 P 1 21 1 4 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 0.016453 0.000000 0.001861 0.00000 SCALE2 0.000000 0.009443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012063 0.00000