HEADER TRANSFERASE 17-JUN-08 3DHD TITLE CRYSTAL STRUCTURE OF HUMAN NAMPT COMPLEXED WITH NICOTINAMIDE TITLE 2 MONONUCLEOTIDE AND PYROPHOSPHATE 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_TAXID: 9606; SOURCE 4 GENE: NAMPT, PBEF, PBEF1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST KEYWDS TRANSFERASE, NMPRTASE, NAMPRTASE, VISFATIN, NMN, NICOTINAMIDE D- KEYWDS 2 RIBONUCLEOTIDE, PYROPHOSPHATE, ALTERNATIVE SPLICING, CYTOPLASM, KEYWDS 3 GLYCOSYLTRANSFERASE, PHOSPHOPROTEIN, POLYMORPHISM, PYRIDINE KEYWDS 4 NUCLEOTIDE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.HO,E.S.BURGOS,S.C.ALMO,V.L.SCHRAMM REVDAT 4 30-AUG-23 3DHD 1 REMARK LINK REVDAT 3 25-OCT-17 3DHD 1 REMARK REVDAT 2 08-SEP-09 3DHD 1 JRNL REVDAT 1 18-AUG-09 3DHD 0 JRNL AUTH E.S.BURGOS,M.C.HO,S.C.ALMO,V.L.SCHRAMM JRNL TITL A PHOSPHOENZYME MIMIC, OVERLAPPING CATALYTIC SITES AND JRNL TITL 2 REACTION COORDINATE MOTION FOR HUMAN NAMPT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 13748 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19666527 JRNL DOI 10.1073/PNAS.0903898106 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 69501 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3460 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3669 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7422 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.177 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.644 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7712 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10477 ; 1.596 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 940 ; 6.184 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 352 ;38.946 ;24.915 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1339 ;14.844 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;13.398 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1150 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5800 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4632 ; 0.868 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7528 ; 1.511 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3080 ; 2.590 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2941 ; 4.102 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3DHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.29000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75507 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.4.0069 REMARK 200 STARTING MODEL: PDB ENTRY 3DGR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM NACL, 100MM TRIS-HCL, 15% PEG REMARK 280 3350, 20% GLYCEROL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 53.53550 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: 8110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 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 MET 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 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 VAL B 95 CB - CA - C ANGL. DEV. = -11.8 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 PRO A 28 150.69 -48.19 REMARK 500 TYR A 231 -53.59 -128.80 REMARK 500 PHE A 269 58.44 -118.05 REMARK 500 TYR A 281 -51.07 -127.75 REMARK 500 GLU A 293 -67.83 -137.34 REMARK 500 ALA A 306 52.09 -144.45 REMARK 500 ASP A 313 32.15 -152.42 REMARK 500 ASP A 416 70.38 -152.30 REMARK 500 TYR B 231 -54.09 -128.23 REMARK 500 PHE B 269 57.96 -119.76 REMARK 500 TYR B 281 -51.34 -130.04 REMARK 500 GLU B 293 -74.59 -129.62 REMARK 500 ASP B 313 26.28 -149.16 REMARK 500 ASP B 416 71.99 -161.27 REMARK 500 ASP B 420 81.46 -154.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 313 OD1 REMARK 620 2 NMN A 503 O3R 85.8 REMARK 620 3 NMN A 503 O2R 97.5 71.1 REMARK 620 4 HOH A 507 O 100.1 169.7 99.7 REMARK 620 5 POP B 504 O6 165.2 87.9 93.1 88.2 REMARK 620 6 POP B 504 O1 81.0 97.3 168.4 91.9 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 POP A 504 O1 REMARK 620 2 POP A 504 O4 87.8 REMARK 620 3 HOH A 508 O 80.6 96.8 REMARK 620 4 HOH A 509 O 89.3 177.0 81.9 REMARK 620 5 HOH B 508 O 104.3 89.0 172.6 92.6 REMARK 620 6 HOH B 509 O 164.1 99.5 84.4 83.1 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 POP A 504 O2 REMARK 620 2 POP A 504 O5 88.8 REMARK 620 3 ASP B 313 OD1 82.4 171.2 REMARK 620 4 NMN B 503 O3R 96.8 96.2 84.9 REMARK 620 5 NMN B 503 O2R 167.4 94.6 94.1 70.8 REMARK 620 6 HOH B 510 O 92.6 88.3 92.1 169.7 99.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 506 O REMARK 620 2 POP B 504 O4 91.3 REMARK 620 3 POP B 504 O3 166.3 86.4 REMARK 620 4 HOH B 505 O 91.4 88.6 102.0 REMARK 620 5 HOH B 506 O 91.0 175.1 90.4 95.7 REMARK 620 6 HOH B 507 O 86.3 92.3 80.4 177.6 83.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DGR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NAMPT COMPLEXED WITH ADP ANALOGUE REMARK 900 RELATED ID: 3DHF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED MIMIC FORM OF HUMAN NAMPT REMARK 900 COMPLEXED WITH NICOTINAMIDE MONONUCLEOTIDE AND PYROPHOSPHATE REMARK 900 RELATED ID: 3DKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NAMPT COMPLEXED WITH BENZAMIDE AND REMARK 900 PHOSPHORIBOSYL PYROPHOSPHATE REMARK 900 RELATED ID: 3DKL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOSPHORYLATED MIMIC FORM OF HUMAN NAMPT REMARK 900 COMPLEXED WITH BENZAMIDE AND PHOSPHORIBOSYL PYROPHOSPHATE DBREF 3DHD A 1 484 UNP P43490 NAMPT_HUMAN 1 484 DBREF 3DHD B 1 484 UNP P43490 NAMPT_HUMAN 1 484 SEQRES 1 A 484 MET ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 A 484 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 A 484 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 A 484 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 A 484 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 A 484 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 A 484 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 A 484 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 A 484 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 A 484 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 A 484 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 A 484 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 A 484 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 A 484 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 A 484 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 A 484 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 A 484 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 A 484 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 A 484 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 A 484 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 A 484 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 A 484 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 A 484 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 A 484 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 A 484 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 A 484 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 A 484 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 A 484 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 A 484 VAL GLU GLY MET LYS GLN LYS MET TRP SER ILE GLU ASN SEQRES 30 A 484 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 A 484 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 A 484 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 A 484 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 A 484 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 A 484 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 A 484 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 A 484 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 A 484 LEU ASN ILE SEQRES 1 B 484 MET ASN PRO ALA ALA GLU ALA GLU PHE ASN ILE LEU LEU SEQRES 2 B 484 ALA THR ASP SER TYR LYS VAL THR HIS TYR LYS GLN TYR SEQRES 3 B 484 PRO PRO ASN THR SER LYS VAL TYR SER TYR PHE GLU CYS SEQRES 4 B 484 ARG GLU LYS LYS THR GLU ASN SER LYS LEU ARG LYS VAL SEQRES 5 B 484 LYS TYR GLU GLU THR VAL PHE TYR GLY LEU GLN TYR ILE SEQRES 6 B 484 LEU ASN LYS TYR LEU LYS GLY LYS VAL VAL THR LYS GLU SEQRES 7 B 484 LYS ILE GLN GLU ALA LYS ASP VAL TYR LYS GLU HIS PHE SEQRES 8 B 484 GLN ASP ASP VAL PHE ASN GLU LYS GLY TRP ASN TYR ILE SEQRES 9 B 484 LEU GLU LYS TYR ASP GLY HIS LEU PRO ILE GLU ILE LYS SEQRES 10 B 484 ALA VAL PRO GLU GLY PHE VAL ILE PRO ARG GLY ASN VAL SEQRES 11 B 484 LEU PHE THR VAL GLU ASN THR ASP PRO GLU CYS TYR TRP SEQRES 12 B 484 LEU THR ASN TRP ILE GLU THR ILE LEU VAL GLN SER TRP SEQRES 13 B 484 TYR PRO ILE THR VAL ALA THR ASN SER ARG GLU GLN LYS SEQRES 14 B 484 LYS ILE LEU ALA LYS TYR LEU LEU GLU THR SER GLY ASN SEQRES 15 B 484 LEU ASP GLY LEU GLU TYR LYS LEU HIS ASP PHE GLY TYR SEQRES 16 B 484 ARG GLY VAL SER SER GLN GLU THR ALA GLY ILE GLY ALA SEQRES 17 B 484 SER ALA HIS LEU VAL ASN PHE LYS GLY THR ASP THR VAL SEQRES 18 B 484 ALA GLY LEU ALA LEU ILE LYS LYS TYR TYR GLY THR LYS SEQRES 19 B 484 ASP PRO VAL PRO GLY TYR SER VAL PRO ALA ALA GLU HIS SEQRES 20 B 484 SER THR ILE THR ALA TRP GLY LYS ASP HIS GLU LYS ASP SEQRES 21 B 484 ALA PHE GLU HIS ILE VAL THR GLN PHE SER SER VAL PRO SEQRES 22 B 484 VAL SER VAL VAL SER ASP SER TYR ASP ILE TYR ASN ALA SEQRES 23 B 484 CYS GLU LYS ILE TRP GLY GLU ASP LEU ARG HIS LEU ILE SEQRES 24 B 484 VAL SER ARG SER THR GLN ALA PRO LEU ILE ILE ARG PRO SEQRES 25 B 484 ASP SER GLY ASN PRO LEU ASP THR VAL LEU LYS VAL LEU SEQRES 26 B 484 GLU ILE LEU GLY LYS LYS PHE PRO VAL THR GLU ASN SER SEQRES 27 B 484 LYS GLY TYR LYS LEU LEU PRO PRO TYR LEU ARG VAL ILE SEQRES 28 B 484 GLN GLY ASP GLY VAL ASP ILE ASN THR LEU GLN GLU ILE SEQRES 29 B 484 VAL GLU GLY MET LYS GLN LYS MET TRP SER ILE GLU ASN SEQRES 30 B 484 ILE ALA PHE GLY SER GLY GLY GLY LEU LEU GLN LYS LEU SEQRES 31 B 484 THR ARG ASP LEU LEU ASN CYS SER PHE LYS CYS SER TYR SEQRES 32 B 484 VAL VAL THR ASN GLY LEU GLY ILE ASN VAL PHE LYS ASP SEQRES 33 B 484 PRO VAL ALA ASP PRO ASN LYS ARG SER LYS LYS GLY ARG SEQRES 34 B 484 LEU SER LEU HIS ARG THR PRO ALA GLY ASN PHE VAL THR SEQRES 35 B 484 LEU GLU GLU GLY LYS GLY ASP LEU GLU GLU TYR GLY GLN SEQRES 36 B 484 ASP LEU LEU HIS THR VAL PHE LYS ASN GLY LYS VAL THR SEQRES 37 B 484 LYS SER TYR SER PHE ASP GLU ILE ARG LYS ASN ALA GLN SEQRES 38 B 484 LEU ASN ILE HET MG A 502 1 HET MG A 501 1 HET NMN A 503 22 HET POP A 504 9 HET MG B 501 1 HET MG B 502 1 HET POP B 504 9 HET NMN B 503 22 HETNAM MG MAGNESIUM ION HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETNAM POP PYROPHOSPHATE 2- HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE FORMUL 3 MG 4(MG 2+) FORMUL 5 NMN 2(C11 H16 N2 O8 P 1+) FORMUL 6 POP 2(H2 O7 P2 2-) FORMUL 11 HOH *359(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 PHE A 91 1 16 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 GLU A 451 5 6 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 TYR B 69 1 9 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 GLY B 181 1 27 HELIX 34 34 GLY B 185 TYR B 188 5 4 HELIX 35 35 SER B 200 LEU B 212 1 13 HELIX 36 36 VAL B 221 TYR B 231 1 11 HELIX 37 37 GLU B 246 ALA B 252 1 7 HELIX 38 38 TRP B 253 ASP B 256 5 4 HELIX 39 39 HIS B 257 PHE B 269 1 13 HELIX 40 40 ASP B 282 LYS B 289 1 8 HELIX 41 41 LEU B 295 VAL B 300 1 6 HELIX 42 42 ASN B 316 PHE B 332 1 17 HELIX 43 43 ASP B 357 LYS B 371 1 15 HELIX 44 44 SER B 374 GLU B 376 5 3 HELIX 45 45 GLY B 383 GLN B 388 1 6 HELIX 46 46 ASP B 420 ARG B 424 5 5 HELIX 47 47 GLY B 446 GLU B 451 5 6 HELIX 48 48 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 VAL A 404 O ILE A 411 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 HIS A 459 N ALA A 118 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 ALA A 379 SHEET 4 C 5 LEU A 308 ARG A 311 1 N ILE A 310 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 PHE B 132 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 VAL B 461 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 OD1 ASP A 313 MG MG A 502 1555 1555 2.23 LINK MG MG A 501 O1 POP A 504 1555 1555 2.05 LINK MG MG A 501 O4 POP A 504 1555 1555 2.09 LINK MG MG A 501 O HOH A 508 1555 1555 2.13 LINK MG MG A 501 O HOH A 509 1555 1555 2.09 LINK MG MG A 501 O HOH B 508 1555 1555 2.11 LINK MG MG A 501 O HOH B 509 1555 1555 2.03 LINK MG MG A 502 O3R NMN A 503 1555 1555 2.50 LINK MG MG A 502 O2R NMN A 503 1555 1555 2.13 LINK MG MG A 502 O HOH A 507 1555 1555 2.06 LINK MG MG A 502 O6 POP B 504 1555 1555 2.02 LINK MG MG A 502 O1 POP B 504 1555 1555 2.38 LINK O2 POP A 504 MG MG B 502 1555 1555 2.28 LINK O5 POP A 504 MG MG B 502 1555 1555 2.02 LINK O HOH A 506 MG MG B 501 1555 1555 2.05 LINK OD1 ASP B 313 MG MG B 502 1555 1555 2.36 LINK MG MG B 501 O4 POP B 504 1555 1555 2.22 LINK MG MG B 501 O3 POP B 504 1555 1555 2.06 LINK MG MG B 501 O HOH B 505 1555 1555 2.19 LINK MG MG B 501 O HOH B 506 1555 1555 2.11 LINK MG MG B 501 O HOH B 507 1555 1555 2.26 LINK MG MG B 502 O3R NMN B 503 1555 1555 2.39 LINK MG MG B 502 O2R NMN B 503 1555 1555 2.21 LINK MG MG B 502 O HOH B 510 1555 1555 1.97 SITE 1 AC2 1 ASP A 313 SITE 1 AC4 1 ASP B 313 SITE 1 AC5 11 PHE A 193 ARG A 196 ASP A 219 ARG A 311 SITE 2 AC5 11 ASP A 313 GLY A 353 GLY A 383 GLY A 384 SITE 3 AC5 11 ASP B 16 TYR B 18 ARG B 392 SITE 1 AC6 7 ARG A 196 ASP A 313 ARG B 40 ARG B 392 SITE 2 AC6 7 LYS B 400 LYS B 415 LYS B 423 SITE 1 AC7 10 TYR A 18 ARG A 392 PHE B 193 ARG B 196 SITE 2 AC7 10 ASP B 219 ARG B 311 ASP B 313 GLY B 353 SITE 3 AC7 10 GLY B 383 GLY B 384 SITE 1 AC8 7 ARG A 40 ARG A 392 LYS A 400 LYS A 415 SITE 2 AC8 7 LYS A 423 ARG B 196 ASP B 313 CRYST1 61.175 107.071 83.336 90.00 97.02 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 0.016347 0.000000 0.002013 0.00000 SCALE2 0.000000 0.009340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012090 0.00000