HEADER HYDROLASE 29-JUL-08 3DZJ
TITLE CRYSTAL STRUCTURE OF HUMAN CD38 EXTRACELLULAR DOMAIN E226Q MUTANT, NMN
TITLE 2 COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ADP-RIBOSYL CYCLASE 1;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: ENZYMATIC DOMAIN: UNP RESIDUES 45-300;
COMPND 5 SYNONYM: CYCLIC ADP-RIBOSE HYDROLASE 1, CADPR HYDROLASE 1, T10, CD38
COMPND 6 ANTIGEN;
COMPND 7 EC: 3.2.2.5;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_TAXID: 9606;
SOURCE 4 GENE: CD38;
SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: X-33 (INVITROGEN);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPICZ(ALPHA)A
KEYWDS NMN COMPLEX, E226Q MUTANT, BETA SHEETS, ALPHA BUNDLE, ALTERNATIVE
KEYWDS 2 SPLICING, DIABETES MELLITUS, GLYCOPROTEIN, HYDROLASE, MEMBRANE, NAD,
KEYWDS 3 POLYMORPHISM, RECEPTOR, SIGNAL-ANCHOR, TRANSMEMBRANE
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.LIU,I.A.KRIKSUNOV,H.JIANG,R.GRAEFF,H.LIN,H.C.LEE,Q.HAO
REVDAT 4 30-AUG-23 3DZJ 1 REMARK
REVDAT 3 20-OCT-21 3DZJ 1 REMARK SEQADV
REVDAT 2 24-FEB-09 3DZJ 1 VERSN
REVDAT 1 04-NOV-08 3DZJ 0
JRNL AUTH Q.LIU,I.A.KRIKSUNOV,H.JIANG,R.GRAEFF,H.LIN,H.C.LEE,Q.HAO
JRNL TITL COVALENT AND NONCOVALENT INTERMEDIATES OF AN NAD UTILIZING
JRNL TITL 2 ENZYME, HUMAN CD38.
JRNL REF CHEM.BIOL. V. 15 1068 2008
JRNL REFN ISSN 1074-5521
JRNL PMID 18940667
JRNL DOI 10.1016/J.CHEMBIOL.2008.08.007
REMARK 2
REMARK 2 RESOLUTION. 1.90 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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 38959
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) : 0.188
REMARK 3 R VALUE (WORKING SET) : 0.185
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2061
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) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2566
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2330
REMARK 3 BIN FREE R VALUE SET COUNT : 138
REMARK 3 BIN FREE R VALUE : 0.2990
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4010
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 44
REMARK 3 SOLVENT ATOMS : 370
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.29
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.06000
REMARK 3 B22 (A**2) : 0.65000
REMARK 3 B33 (A**2) : 1.09000
REMARK 3 B12 (A**2) : 0.56000
REMARK 3 B13 (A**2) : 0.45000
REMARK 3 B23 (A**2) : 0.98000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.163
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.106
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4168 ; 0.019 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5654 ; 1.772 ; 1.945
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 6.390 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;36.316 ;23.958
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 710 ;15.779 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.826 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.129 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3150 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1949 ; 0.228 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2826 ; 0.314 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 323 ; 0.163 ; 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): 37 ; 0.152 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.109 ; 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): 2569 ; 1.210 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4050 ; 1.889 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1844 ; 2.975 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1604 ; 4.537 ; 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 : BABINET MODEL WITH 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 3DZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-08.
REMARK 100 THE DEPOSITION ID IS D_1000048685.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-FEB-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CHESS
REMARK 200 BEAMLINE : A1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41633
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.09000
REMARK 200 R SYM (I) : 0.09000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000
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) : 1.98
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : 0.43600
REMARK 200 R SYM FOR SHELL (I) : 0.43600
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1YH3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.61
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.0, 15% PEG 4000, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 LYS A 39
REMARK 465 ARG A 40
REMARK 465 GLU A 41
REMARK 465 ALA A 42
REMARK 465 GLU A 43
REMARK 465 ALA A 44
REMARK 465 THR A 297
REMARK 465 SER A 298
REMARK 465 GLU A 299
REMARK 465 ILE A 300
REMARK 465 LYS B 39
REMARK 465 ARG B 40
REMARK 465 GLU B 41
REMARK 465 ALA B 42
REMARK 465 GLU B 43
REMARK 465 ALA B 44
REMARK 465 THR B 297
REMARK 465 SER B 298
REMARK 465 GLU B 299
REMARK 465 ILE B 300
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 247 CB CG CD NE CZ NH1 NH2
REMARK 470 GLU A 248 CB CG CD OE1 OE2
REMARK 470 ASP A 249 CB CG OD1 OD2
REMARK 470 ARG A 280 CB CG CD NE CZ NH1 NH2
REMARK 470 ASN A 290 CG OD1 ND2
REMARK 470 PRO A 291 CB CG CD
REMARK 470 GLU A 292 CB CG CD OE1 OE2
REMARK 470 ASP A 293 CB CG OD1 OD2
REMARK 470 SER A 294 CB OG
REMARK 470 SER A 295 CB OG
REMARK 470 ARG B 247 CB CG CD NE CZ NH1 NH2
REMARK 470 GLU B 248 CB CG CD OE1 OE2
REMARK 470 ASP B 249 CB CG OD1 OD2
REMARK 470 ARG B 280 CB CG CD NE CZ NH1 NH2
REMARK 470 ASN B 290 CG OD1 ND2
REMARK 470 PRO B 291 CB CG CD
REMARK 470 GLU B 292 CB CG CD OE1 OE2
REMARK 470 ASP B 293 CB CG OD1 OD2
REMARK 470 SER B 294 CB OG
REMARK 470 SER B 295 CB OG
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 LYS B 283 C LYS B 283 O 0.138
REMARK 500 CYS B 296 C CYS B 296 O 0.139
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 GLN A 48 150.47 75.88
REMARK 500 ARG A 127 -46.93 72.90
REMARK 500 ARG A 140 11.82 -65.68
REMARK 500 ASP A 179 -65.49 -108.59
REMARK 500 ASN A 182 46.02 -92.22
REMARK 500 ASP A 202 -117.87 63.63
REMARK 500 ARG A 212 -97.63 -61.45
REMARK 500 SER A 213 -47.99 169.64
REMARK 500 ARG A 247 127.81 134.60
REMARK 500 GLU A 248 -119.41 -69.36
REMARK 500 GLU A 292 152.73 58.60
REMARK 500 ASP A 293 163.48 62.71
REMARK 500 SER A 294 -171.11 66.95
REMARK 500 SER A 295 36.65 -80.41
REMARK 500 ARG B 127 -23.48 61.69
REMARK 500 ASP B 179 -75.51 -109.39
REMARK 500 ASN B 182 57.41 -91.04
REMARK 500 ASP B 202 -120.86 68.19
REMARK 500 SER B 213 -50.43 76.91
REMARK 500 ASP B 249 58.39 -98.61
REMARK 500 ASN B 270 50.31 72.53
REMARK 500 GLU B 292 100.32 65.50
REMARK 500 ASP B 293 85.52 140.68
REMARK 500 SER B 294 72.59 110.35
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 ALA B 164 THR B 165 -149.16
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 NMN A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN B 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3DZF RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, ARA-2-DEOXY-2-FLUORO-RIBOSE-5'-
REMARK 900 PHOSPHATE COMPLEX
REMARK 900 RELATED ID: 3DZG RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, ARA-2-DEOXY-2-FLUORO-RIBOSE-5'-
REMARK 900 PHOSPHATE/NICOTINAMIDE COMPLEX
REMARK 900 RELATED ID: 3DZH RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, GTP COMPLEX
REMARK 900 RELATED ID: 3DZI RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, RIBOSE-5'-PHOSPHATE INTERMEDIATE/
REMARK 900 GTP COMPLEX
REMARK 900 RELATED ID: 3DZK RELATED DB: PDB
REMARK 900 HUMAN CD38 EXTRACELLULAR DOMAIN, NMN COMPLEX
DBREF 3DZJ A 45 300 UNP P28907 CD38_HUMAN 45 300
DBREF 3DZJ B 45 300 UNP P28907 CD38_HUMAN 45 300
SEQADV 3DZJ LYS A 39 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ARG A 40 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ GLU A 41 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ALA A 42 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ GLU A 43 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ALA A 44 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ THR A 49 UNP P28907 GLN 49 ENGINEERED MUTATION
SEQADV 3DZJ ASP A 100 UNP P28907 ASN 100 ENGINEERED MUTATION
SEQADV 3DZJ ALA A 164 UNP P28907 ASN 164 ENGINEERED MUTATION
SEQADV 3DZJ ASP A 209 UNP P28907 ASN 209 ENGINEERED MUTATION
SEQADV 3DZJ ASP A 219 UNP P28907 ASN 219 ENGINEERED MUTATION
SEQADV 3DZJ GLN A 226 UNP P28907 GLU 226 ENGINEERED MUTATION
SEQADV 3DZJ LYS B 39 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ARG B 40 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ GLU B 41 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ALA B 42 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ GLU B 43 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ ALA B 44 UNP P28907 EXPRESSION TAG
SEQADV 3DZJ THR B 49 UNP P28907 GLN 49 ENGINEERED MUTATION
SEQADV 3DZJ ASP B 100 UNP P28907 ASN 100 ENGINEERED MUTATION
SEQADV 3DZJ ALA B 164 UNP P28907 ASN 164 ENGINEERED MUTATION
SEQADV 3DZJ ASP B 209 UNP P28907 ASN 209 ENGINEERED MUTATION
SEQADV 3DZJ ASP B 219 UNP P28907 ASN 219 ENGINEERED MUTATION
SEQADV 3DZJ GLN B 226 UNP P28907 GLU 226 ENGINEERED MUTATION
SEQRES 1 A 262 LYS ARG GLU ALA GLU ALA ARG TRP ARG GLN THR TRP SER
SEQRES 2 A 262 GLY PRO GLY THR THR LYS ARG PHE PRO GLU THR VAL LEU
SEQRES 3 A 262 ALA ARG CYS VAL LYS TYR THR GLU ILE HIS PRO GLU MET
SEQRES 4 A 262 ARG HIS VAL ASP CYS GLN SER VAL TRP ASP ALA PHE LYS
SEQRES 5 A 262 GLY ALA PHE ILE SER LYS HIS PRO CYS ASP ILE THR GLU
SEQRES 6 A 262 GLU ASP TYR GLN PRO LEU MET LYS LEU GLY THR GLN THR
SEQRES 7 A 262 VAL PRO CYS ASN LYS ILE LEU LEU TRP SER ARG ILE LYS
SEQRES 8 A 262 ASP LEU ALA HIS GLN PHE THR GLN VAL GLN ARG ASP MET
SEQRES 9 A 262 PHE THR LEU GLU ASP THR LEU LEU GLY TYR LEU ALA ASP
SEQRES 10 A 262 ASP LEU THR TRP CYS GLY GLU PHE ALA THR SER LYS ILE
SEQRES 11 A 262 ASN TYR GLN SER CYS PRO ASP TRP ARG LYS ASP CYS SER
SEQRES 12 A 262 ASN ASN PRO VAL SER VAL PHE TRP LYS THR VAL SER ARG
SEQRES 13 A 262 ARG PHE ALA GLU ALA ALA CYS ASP VAL VAL HIS VAL MET
SEQRES 14 A 262 LEU ASP GLY SER ARG SER LYS ILE PHE ASP LYS ASP SER
SEQRES 15 A 262 THR PHE GLY SER VAL GLN VAL HIS ASN LEU GLN PRO GLU
SEQRES 16 A 262 LYS VAL GLN THR LEU GLU ALA TRP VAL ILE HIS GLY GLY
SEQRES 17 A 262 ARG GLU ASP SER ARG ASP LEU CYS GLN ASP PRO THR ILE
SEQRES 18 A 262 LYS GLU LEU GLU SER ILE ILE SER LYS ARG ASN ILE GLN
SEQRES 19 A 262 PHE SER CYS LYS ASN ILE TYR ARG PRO ASP LYS PHE LEU
SEQRES 20 A 262 GLN CYS VAL LYS ASN PRO GLU ASP SER SER CYS THR SER
SEQRES 21 A 262 GLU ILE
SEQRES 1 B 262 LYS ARG GLU ALA GLU ALA ARG TRP ARG GLN THR TRP SER
SEQRES 2 B 262 GLY PRO GLY THR THR LYS ARG PHE PRO GLU THR VAL LEU
SEQRES 3 B 262 ALA ARG CYS VAL LYS TYR THR GLU ILE HIS PRO GLU MET
SEQRES 4 B 262 ARG HIS VAL ASP CYS GLN SER VAL TRP ASP ALA PHE LYS
SEQRES 5 B 262 GLY ALA PHE ILE SER LYS HIS PRO CYS ASP ILE THR GLU
SEQRES 6 B 262 GLU ASP TYR GLN PRO LEU MET LYS LEU GLY THR GLN THR
SEQRES 7 B 262 VAL PRO CYS ASN LYS ILE LEU LEU TRP SER ARG ILE LYS
SEQRES 8 B 262 ASP LEU ALA HIS GLN PHE THR GLN VAL GLN ARG ASP MET
SEQRES 9 B 262 PHE THR LEU GLU ASP THR LEU LEU GLY TYR LEU ALA ASP
SEQRES 10 B 262 ASP LEU THR TRP CYS GLY GLU PHE ALA THR SER LYS ILE
SEQRES 11 B 262 ASN TYR GLN SER CYS PRO ASP TRP ARG LYS ASP CYS SER
SEQRES 12 B 262 ASN ASN PRO VAL SER VAL PHE TRP LYS THR VAL SER ARG
SEQRES 13 B 262 ARG PHE ALA GLU ALA ALA CYS ASP VAL VAL HIS VAL MET
SEQRES 14 B 262 LEU ASP GLY SER ARG SER LYS ILE PHE ASP LYS ASP SER
SEQRES 15 B 262 THR PHE GLY SER VAL GLN VAL HIS ASN LEU GLN PRO GLU
SEQRES 16 B 262 LYS VAL GLN THR LEU GLU ALA TRP VAL ILE HIS GLY GLY
SEQRES 17 B 262 ARG GLU ASP SER ARG ASP LEU CYS GLN ASP PRO THR ILE
SEQRES 18 B 262 LYS GLU LEU GLU SER ILE ILE SER LYS ARG ASN ILE GLN
SEQRES 19 B 262 PHE SER CYS LYS ASN ILE TYR ARG PRO ASP LYS PHE LEU
SEQRES 20 B 262 GLN CYS VAL LYS ASN PRO GLU ASP SER SER CYS THR SER
SEQRES 21 B 262 GLU ILE
HET NMN A 301 22
HET NMN B 301 22
HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE
FORMUL 3 NMN 2(C11 H16 N2 O8 P 1+)
FORMUL 5 HOH *370(H2 O)
HELIX 1 1 ARG A 58 HIS A 74 1 17
HELIX 2 2 PRO A 75 ARG A 78 5 4
HELIX 3 3 ASP A 81 ILE A 94 1 14
HELIX 4 4 THR A 102 ASP A 105 5 4
HELIX 5 5 TYR A 106 GLY A 113 1 8
HELIX 6 6 LYS A 129 GLN A 139 1 11
HELIX 7 7 THR A 144 ASP A 147 5 4
HELIX 8 8 THR A 148 ASP A 155 1 8
HELIX 9 9 ASN A 183 ALA A 200 1 18
HELIX 10 10 SER A 220 VAL A 225 1 6
HELIX 11 11 ASP A 252 GLN A 255 5 4
HELIX 12 12 ASP A 256 ARG A 269 1 14
HELIX 13 13 ARG A 280 ASN A 290 1 11
HELIX 14 14 ARG B 58 HIS B 74 1 17
HELIX 15 15 PRO B 75 ARG B 78 5 4
HELIX 16 16 ASP B 81 ILE B 94 1 14
HELIX 17 17 THR B 102 ASP B 105 5 4
HELIX 18 18 TYR B 106 GLY B 113 1 8
HELIX 19 19 ILE B 128 GLN B 139 1 12
HELIX 20 20 THR B 144 ASP B 147 5 4
HELIX 21 21 THR B 148 ASP B 155 1 8
HELIX 22 22 ASN B 183 ALA B 199 1 17
HELIX 23 23 SER B 220 VAL B 225 1 6
HELIX 24 24 GLN B 226 LEU B 230 5 5
HELIX 25 25 ASP B 252 GLN B 255 5 4
HELIX 26 26 ASP B 256 ARG B 269 1 14
HELIX 27 27 ARG B 280 ASN B 290 1 11
SHEET 1 A 2 GLY A 52 PRO A 53 0
SHEET 2 A 2 SER A 172 CYS A 173 -1 O CYS A 173 N GLY A 52
SHEET 1 B 4 LEU A 123 SER A 126 0
SHEET 2 B 4 ASP A 202 ASP A 209 1 O HIS A 205 N LEU A 124
SHEET 3 B 4 VAL A 235 ILE A 243 1 O ILE A 243 N LEU A 208
SHEET 4 B 4 GLN A 272 ILE A 278 1 O ILE A 278 N VAL A 242
SHEET 1 C 2 GLY B 52 PRO B 53 0
SHEET 2 C 2 SER B 172 CYS B 173 -1 O CYS B 173 N GLY B 52
SHEET 1 D 4 LEU B 123 SER B 126 0
SHEET 2 D 4 ASP B 202 ASP B 209 1 O HIS B 205 N LEU B 124
SHEET 3 D 4 VAL B 235 ILE B 243 1 O TRP B 241 N VAL B 206
SHEET 4 D 4 GLN B 272 ILE B 278 1 O LYS B 276 N ALA B 240
SSBOND 1 CYS A 67 CYS A 82 1555 1555 2.11
SSBOND 2 CYS A 99 CYS A 180 1555 1555 2.10
SSBOND 3 CYS A 119 CYS A 201 1555 1555 2.07
SSBOND 4 CYS A 160 CYS A 173 1555 1555 2.11
SSBOND 5 CYS A 254 CYS A 275 1555 1555 2.12
SSBOND 6 CYS A 287 CYS A 296 1555 1555 2.03
SSBOND 7 CYS B 67 CYS B 82 1555 1555 2.12
SSBOND 8 CYS B 99 CYS B 180 1555 1555 2.07
SSBOND 9 CYS B 119 CYS B 201 1555 1555 2.07
SSBOND 10 CYS B 160 CYS B 173 1555 1555 2.18
SSBOND 11 CYS B 254 CYS B 275 1555 1555 2.05
SSBOND 12 CYS B 287 CYS B 296 1555 1555 2.05
SITE 1 AC1 17 LEU A 124 TRP A 125 SER A 126 ARG A 127
SITE 2 AC1 17 LEU A 145 GLU A 146 ASP A 155 TRP A 189
SITE 3 AC1 17 SER A 193 SER A 220 THR A 221 PHE A 222
SITE 4 AC1 17 GLN A 226 HOH A 302 HOH A 328 HOH A 342
SITE 5 AC1 17 HOH A 487
SITE 1 AC2 15 TRP B 125 SER B 126 ARG B 127 LEU B 145
SITE 2 AC2 15 GLU B 146 ASP B 155 TRP B 189 SER B 193
SITE 3 AC2 15 SER B 220 THR B 221 PHE B 222 GLN B 226
SITE 4 AC2 15 HOH B 403 HOH B 419 HOH B 433
CRYST1 41.858 53.228 65.670 106.11 91.97 95.03 P 1 2
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 0.023890 0.002103 0.001472 0.00000
SCALE2 0.000000 0.018860 0.005540 0.00000
SCALE3 0.000000 0.000000 0.015880 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
