HEADER OXIDOREDUCTASE 14-JUL-10 3NXO
TITLE PERFERENTIAL SELECTION OF ISOMER BINDING FROM CHIRAL MIXTURES:
TITLE 2 ALTERNATE BINDING MODES OBSERVED FOR THE E- AND Z-ISOMERS OF A SERIES
TITLE 3 OF 5-SUBSTITUTED 2,4-DIAMINOFURO[2,3-D]PYRIMIDINES AS TERNARY
TITLE 4 COMPLEXES WITH NADPH AND HUMAN DIHYDROFOLATE REDUCTASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 1.5.1.3;
COMPND 5 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: DHFR, DHFRP1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS E-Z-ISOMERS BINDING PREFERENCES, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CODY
REVDAT 4 06-SEP-23 3NXO 1 REMARK SEQADV
REVDAT 3 08-NOV-17 3NXO 1 REMARK
REVDAT 2 21-MAR-12 3NXO 1 JRNL VERSN
REVDAT 1 01-DEC-10 3NXO 0
JRNL AUTH V.CODY,J.PIRAINO,J.PACE,W.LI,A.GANGJEE
JRNL TITL PREFERENTIAL SELECTION OF ISOMER BINDING FROM CHIRAL
JRNL TITL 2 MIXTURES: ALTERNATE BINDING MODES OBSERVED FOR THE E AND Z
JRNL TITL 3 ISOMERS OF A SERIES OF 5-SUBSTITUTED
JRNL TITL 4 2,4-DIAMINOFURO[2,3-D]PYRIMIDINES AS TERNARY COMPLEXES WITH
JRNL TITL 5 NADPH AND HUMAN DIHYDROFOLATE REDUCTASE.
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 1271 2010
JRNL REFN ISSN 0907-4449
JRNL PMID 21123866
JRNL DOI 10.1107/S0907444910035808
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0088
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) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.62
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 42917
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) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.209
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2276
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) : 1.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3163
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.2920
REMARK 3 BIN FREE R VALUE SET COUNT : 176
REMARK 3 BIN FREE R VALUE : 0.3470
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1504
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 97
REMARK 3 SOLVENT ATOMS : 165
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.68
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.822
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1686 ; 0.034 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2301 ; 2.788 ; 2.049
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 197 ; 7.071 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 73 ;37.888 ;24.932
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 296 ;14.454 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.495 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 241 ; 0.176 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1267 ; 0.015 ; 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): 965 ; 1.492 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1576 ; 2.491 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 721 ; 3.618 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 725 ; 5.297 ; 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 : 1.40
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 3NXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10.
REMARK 100 THE DEPOSITION ID IS D_1000060408.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-DEC-08
REMARK 200 TEMPERATURE (KELVIN) : 200.0
REMARK 200 PH : 6.9
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL9-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.975
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45197
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 26.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 8.700
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : 0.02500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 8.20
REMARK 200 R MERGE FOR SHELL (I) : 0.50000
REMARK 200 R SYM FOR SHELL (I) : 0.17000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400
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 1U70.PDB
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.51
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: K2PO4 WITH 30% SATURATED AMMONIUM
REMARK 280 SULFATE WITH 3% V/V ETHANOL, PH 6.9, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 X+2/3,Y+1/3,Z+1/3
REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3
REMARK 290 7555 X+1/3,Y+2/3,Z+2/3
REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.07500
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.29201
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.98933
REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 42.07500
REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.29201
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.98933
REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 42.07500
REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.29201
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.98933
REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.58403
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 51.97867
REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 48.58403
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 51.97867
REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 48.58403
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 51.97867
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: 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 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 CB THR A 146 O HOH A 344 1.32
REMARK 500 OG1 THR A 146 O HOH A 344 1.98
REMARK 500 O ARG A 63 N ARG A 65 2.13
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 195 O HOH A 334 6555 1.34
REMARK 500
REMARK 500 REMARK: NULL
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 MET A 14 SD MET A 14 CE -0.411
REMARK 500 ARG A 63 C ARG A 63 O -0.125
REMARK 500 MET A 111 SD MET A 111 CE -0.487
REMARK 500 TYR A 156 CE1 TYR A 156 CZ -0.082
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 LEU A 22 CB - CG - CD1 ANGL. DEV. = -17.0 DEGREES
REMARK 500 ARG A 65 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ARG A 65 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 MET A 139 CG - SD - CE ANGL. DEV. = -17.1 DEGREES
REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = 8.2 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 ARG A 63 -133.57 -63.91
REMARK 500 ASN A 64 -20.47 40.57
REMARK 500 ASP A 110 -99.28 -90.85
REMARK 500 MET A 139 37.18 -88.61
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 D2B A 187
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 188
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 189
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 190
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 191
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 192
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 193
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3NXR RELATED DB: PDB
REMARK 900 RELATED ID: 3NXT RELATED DB: PDB
REMARK 900 RELATED ID: 3NXV RELATED DB: PDB
REMARK 900 RELATED ID: 3NXX RELATED DB: PDB
REMARK 900 RELATED ID: 3NXY RELATED DB: PDB
REMARK 900 RELATED ID: 3NZ6 RELATED DB: PDB
REMARK 900 RELATED ID: 3NZ9 RELATED DB: PDB
REMARK 900 RELATED ID: 3NZA RELATED DB: PDB
REMARK 900 RELATED ID: 3NZB RELATED DB: PDB
REMARK 900 RELATED ID: 3NZC RELATED DB: PDB
REMARK 900 RELATED ID: 3NZD RELATED DB: PDB
REMARK 900 RELATED ID: 3GYF RELATED DB: PDB
REMARK 900 Z-ISOMER WITH HDHFR
REMARK 900 RELATED ID: 3D7Y RELATED DB: PDB
REMARK 900 Z-ISOMER WITH MOUSE DHFR
REMARK 900 RELATED ID: 3D7X RELATED DB: PDB
REMARK 900 E-ISOMER WITH MOUSE DHFR
DBREF 3NXO A 1 186 UNP P00374 DYR_HUMAN 2 187
SEQADV 3NXO ARG A 63 UNP P00374 LYS 64 CONFLICT
SEQRES 1 A 186 VAL GLY SER LEU ASN CYS ILE VAL ALA VAL SER GLN ASN
SEQRES 2 A 186 MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO PRO
SEQRES 3 A 186 LEU ARG ASN GLU PHE ARG TYR PHE GLN ARG MET THR THR
SEQRES 4 A 186 THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE MET
SEQRES 5 A 186 GLY LYS LYS THR TRP PHE SER ILE PRO GLU ARG ASN ARG
SEQRES 6 A 186 PRO LEU LYS GLY ARG ILE ASN LEU VAL LEU SER ARG GLU
SEQRES 7 A 186 LEU LYS GLU PRO PRO GLN GLY ALA HIS PHE LEU SER ARG
SEQRES 8 A 186 SER LEU ASP ASP ALA LEU LYS LEU THR GLU GLN PRO GLU
SEQRES 9 A 186 LEU ALA ASN LYS VAL ASP MET VAL TRP ILE VAL GLY GLY
SEQRES 10 A 186 SER SER VAL TYR LYS GLU ALA MET ASN HIS PRO GLY HIS
SEQRES 11 A 186 LEU LYS LEU PHE VAL THR ARG ILE MET GLN ASP PHE GLU
SEQRES 12 A 186 SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLU LYS TYR
SEQRES 13 A 186 LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER ASP VAL
SEQRES 14 A 186 GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL TYR
SEQRES 15 A 186 GLU LYS ASN ASP
HET D2B A 187 24
HET SO4 A 188 5
HET SO4 A 189 5
HET SO4 A 190 5
HET SO4 A 191 5
HET SO4 A 192 5
HET NDP A 193 48
HETNAM D2B 5-[(1Z)-2-(2-METHOXYPHENYL)-3-METHYLBUT-1-EN-1-
HETNAM 2 D2B YL]FURO[2,3-D]PYRIMIDINE-2,4-DIAMINE
HETNAM SO4 SULFATE ION
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
FORMUL 2 D2B C18 H20 N4 O2
FORMUL 3 SO4 5(O4 S 2-)
FORMUL 8 NDP C21 H30 N7 O17 P3
FORMUL 9 HOH *165(H2 O)
HELIX 1 1 LEU A 27 THR A 40 1 14
HELIX 2 2 LYS A 54 ILE A 60 1 7
HELIX 3 3 SER A 92 GLN A 102 1 11
HELIX 4 4 GLY A 117 ASN A 126 1 10
SHEET 1 A 8 PHE A 88 SER A 90 0
SHEET 2 A 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88
SHEET 3 A 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71
SHEET 4 A 8 VAL A 109 ILE A 114 1 O TRP A 113 N LEU A 49
SHEET 5 A 8 LEU A 4 SER A 11 1 N ASN A 5 O ILE A 114
SHEET 6 A 8 HIS A 130 ILE A 138 1 O PHE A 134 N CYS A 6
SHEET 7 A 8 ILE A 175 ASN A 185 -1 O TYR A 182 N LEU A 133
SHEET 8 A 8 LYS A 157 LEU A 158 -1 N LYS A 157 O GLU A 183
SHEET 1 B 8 PHE A 88 SER A 90 0
SHEET 2 B 8 ILE A 71 LEU A 75 1 N VAL A 74 O PHE A 88
SHEET 3 B 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71
SHEET 4 B 8 VAL A 109 ILE A 114 1 O TRP A 113 N LEU A 49
SHEET 5 B 8 LEU A 4 SER A 11 1 N ASN A 5 O ILE A 114
SHEET 6 B 8 HIS A 130 ILE A 138 1 O PHE A 134 N CYS A 6
SHEET 7 B 8 ILE A 175 ASN A 185 -1 O TYR A 182 N LEU A 133
SHEET 8 B 8 GLN A 170 GLU A 172 -1 N GLN A 170 O TYR A 177
SHEET 1 C 2 GLY A 15 GLY A 17 0
SHEET 2 C 2 THR A 146 PHE A 147 -1 O THR A 146 N ILE A 16
CISPEP 1 ARG A 65 PRO A 66 0 10.04
CISPEP 2 GLY A 116 GLY A 117 0 8.03
SITE 1 AC1 12 ILE A 7 VAL A 8 ALA A 9 GLU A 30
SITE 2 AC1 12 PHE A 31 PHE A 34 THR A 56 SER A 59
SITE 3 AC1 12 ILE A 60 VAL A 115 THR A 136 NDP A 193
SITE 1 AC2 3 GLU A 62 ARG A 65 HOH A 296
SITE 1 AC3 4 LYS A 122 PRO A 149 GLU A 150 HOH A 259
SITE 1 AC4 5 GLU A 143 SER A 167 SO4 A 191 HOH A 284
SITE 2 AC4 5 HOH A 313
SITE 1 AC5 4 GLU A 143 LEU A 166 SER A 167 SO4 A 190
SITE 1 AC6 7 SER A 118 THR A 146 LYS A 178 NDP A 193
SITE 2 AC6 7 HOH A 220 HOH A 249 HOH A 349
SITE 1 AC7 36 VAL A 8 ALA A 9 ILE A 16 GLY A 17
SITE 2 AC7 36 GLY A 20 ASP A 21 LEU A 22 GLY A 53
SITE 3 AC7 36 LYS A 54 LYS A 55 THR A 56 SER A 59
SITE 4 AC7 36 LEU A 75 SER A 76 ARG A 77 GLU A 78
SITE 5 AC7 36 ARG A 91 SER A 92 VAL A 115 GLY A 116
SITE 6 AC7 36 GLY A 117 SER A 118 SER A 119 VAL A 120
SITE 7 AC7 36 TYR A 121 GLU A 123 D2B A 187 SO4 A 192
SITE 8 AC7 36 HOH A 206 HOH A 250 HOH A 252 HOH A 294
SITE 9 AC7 36 HOH A 298 HOH A 304 HOH A 330 HOH A 351
CRYST1 84.150 84.150 77.968 90.00 90.00 120.00 H 3 9
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 0.011884 0.006861 0.000000 0.00000
SCALE2 0.000000 0.013722 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012826 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
