HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 16-JUL-10 3NZC
TITLE STRUCTURAL ANALYSIS OF PNEUMOCYSTIS CARINII AND HUMAN DHFR COMPLEXES
TITLE 2 WITH NADPH AND A SERIES OF FIVE POTENT 5-(OMEGA-CARBOXY(ALKYLOXY)
TITLE 3 PYRIDO[2,3-D]PYRIDINE DERIVATIVEA
CAVEAT 3NZC C-N BOND DISTANCES BETWEEN RESIDUES GLN 4 AND LYS 5 AND
CAVEAT 2 3NZC BETWEEN RESIDUES ILE 92 AND HIS 93 ARE OUTSIDE OF THE
CAVEAT 3 3NZC ACCEPTED RANGE FOR THE PEPTIDE BOND
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE;
COMPND 3 CHAIN: X;
COMPND 4 EC: 1.5.1.3;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PNEUMOCYSTIS CARINII;
SOURCE 3 ORGANISM_TAXID: 4754;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS PNEUMOCYSTIS CARINII DHFR INHIBITOR COMPLEXES, OXIDOREDUCTASE,
KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CODY
REVDAT 4 06-SEP-23 3NZC 1 REMARK
REVDAT 3 08-NOV-17 3NZC 1 REMARK
REVDAT 2 12-JAN-11 3NZC 1 DBREF JRNL
REVDAT 1 29-DEC-10 3NZC 0
JRNL AUTH V.CODY,J.PACE
JRNL TITL STRUCTURAL ANALYSIS OF PNEUMOCYSTIS CARINII AND HUMAN DHFR
JRNL TITL 2 COMPLEXES WITH NADPH AND A SERIES OF FIVE POTENT
JRNL TITL 3 6-[5'-([OMEGA]-CARBOXYALKOXY)BENZYL]PYRIDO[2,3-D]PYRIMIDINE
JRNL TITL 4 DERIVATIVES
JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 1 2011
JRNL REFN ISSN 0907-4449
JRNL PMID 21206056
JRNL DOI 10.1107/S0907444910041004
REMARK 2
REMARK 2 RESOLUTION. 2.00 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) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.51
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 11845
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) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.209
REMARK 3 FREE R VALUE : 0.260
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 636
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) : 915
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69
REMARK 3 BIN R VALUE (WORKING SET) : 0.2170
REMARK 3 BIN FREE R VALUE SET COUNT : 40
REMARK 3 BIN FREE R VALUE : 0.3020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1686
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 48
REMARK 3 SOLVENT ATOMS : 48
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.20
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.03000
REMARK 3 B22 (A**2) : -0.07000
REMARK 3 B33 (A**2) : 0.04000
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): 0.200
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.917
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1656 ; 0.023 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2235 ; 2.124 ; 1.970
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 190 ; 9.300 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;31.629 ;22.676
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 299 ;19.205 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.127 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 237 ; 0.178 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1226 ; 0.010 ; 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): 956 ; 1.418 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1554 ; 2.462 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 700 ; 3.333 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 681 ; 5.094 ; 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 3NZC 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_1000060468.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-JUN-06
REMARK 200 TEMPERATURE (KELVIN) : 200
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL11-1
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 : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16731
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : 0.06500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.0730
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.30
REMARK 200 R MERGE FOR SHELL (I) : 0.34000
REMARK 200 R SYM FOR SHELL (I) : 0.41000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200
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 3CD2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30-36% PEG 2K, 46-52 MM MES, 100 MM
REMARK 280 KCL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273K
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 21.33350
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: X
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 475
REMARK 475 ZERO OCCUPANCY RESIDUES
REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY.
REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT
REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE)
REMARK 475 M RES C SSEQI
REMARK 475 MET X 1
REMARK 475 ASN X 2
REMARK 475 GLN X 3
REMARK 475 GLN X 4
REMARK 475 ASN X 83
REMARK 475 GLU X 84
REMARK 475 SER X 85
REMARK 475 LEU X 86
REMARK 475 ASP X 87
REMARK 475 LEU X 88
REMARK 475 GLY X 89
REMARK 475 ASN X 90
REMARK 475 GLY X 91
REMARK 475 ILE X 92
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 ILE X 92 N HIS X 93 1.51
REMARK 500 OE2 GLU X 103 NH2 ARG X 107 1.78
REMARK 500 CA GLY X 125 O3 PO4 X 208 1.98
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 GLN X 4 C LYS X 5 N -0.256
REMARK 500 ILE X 92 C HIS X 93 N -0.500
REMARK 500 PHE X 156 CE1 PHE X 156 CZ 0.119
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 X 9 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES
REMARK 500 ARG X 82 O - C - N ANGL. DEV. = -11.5 DEGREES
REMARK 500 ILE X 92 CA - C - N ANGL. DEV. = 26.5 DEGREES
REMARK 500 ILE X 92 O - C - N ANGL. DEV. = -32.3 DEGREES
REMARK 500 HIS X 93 C - N - CA ANGL. DEV. = 39.6 DEGREES
REMARK 500 LEU X 128 CB - CG - CD2 ANGL. DEV. = 10.3 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 X 2 -30.19 150.10
REMARK 500 GLN X 3 56.32 -119.16
REMARK 500 ARG X 21 -98.20 -123.93
REMARK 500 ASN X 23 23.86 90.98
REMARK 500 PRO X 26 44.24 -79.10
REMARK 500 LEU X 67 -36.21 -36.27
REMARK 500 ARG X 82 19.63 -67.20
REMARK 500 GLU X 84 94.86 -41.67
REMARK 500 SER X 85 -100.16 -53.81
REMARK 500 LEU X 86 -148.93 -128.04
REMARK 500 ASP X 87 -8.67 -176.05
REMARK 500 LEU X 88 -116.50 38.62
REMARK 500 ASN X 90 77.30 -51.71
REMARK 500 HIS X 93 120.57 -174.78
REMARK 500 ASN X 118 -89.73 -89.39
REMARK 500 ASP X 193 58.12 33.85
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 PRO X 44 THR X 45 -149.71
REMARK 500 GLY X 91 ILE X 92 -149.35
REMARK 500 ILE X 92 HIS X 93 -61.13
REMARK 500 GLY X 124 GLY X 125 -116.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 ARG X 82 -15.48
REMARK 500 ILE X 92 -11.58
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 D2O X 207
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 X 208
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL X 210
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3NXO RELATED DB: PDB
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: 3NZD RELATED DB: PDB
REMARK 900 RELATED ID: 2FZH RELATED DB: PDB
REMARK 900 RELATED ID: 2FZI RELATED DB: PDB
REMARK 900 RELATED ID: 2FZJ RELATED DB: PDB
DBREF 3NZC X 1 206 UNP P16184 DYR_PNECA 1 206
SEQRES 1 X 206 MET ASN GLN GLN LYS SER LEU THR LEU ILE VAL ALA LEU
SEQRES 2 X 206 THR THR SER TYR GLY ILE GLY ARG SER ASN SER LEU PRO
SEQRES 3 X 206 TRP LYS LEU LYS LYS GLU ILE SER TYR PHE LYS ARG VAL
SEQRES 4 X 206 THR SER PHE VAL PRO THR PHE ASP SER PHE GLU SER MET
SEQRES 5 X 206 ASN VAL VAL LEU MET GLY ARG LYS THR TRP GLU SER ILE
SEQRES 6 X 206 PRO LEU GLN PHE ARG PRO LEU LYS GLY ARG ILE ASN VAL
SEQRES 7 X 206 VAL ILE THR ARG ASN GLU SER LEU ASP LEU GLY ASN GLY
SEQRES 8 X 206 ILE HIS SER ALA LYS SER LEU ASP HIS ALA LEU GLU LEU
SEQRES 9 X 206 LEU TYR ARG THR TYR GLY SER GLU SER SER VAL GLN ILE
SEQRES 10 X 206 ASN ARG ILE PHE VAL ILE GLY GLY ALA GLN LEU TYR LYS
SEQRES 11 X 206 ALA ALA MET ASP HIS PRO LYS LEU ASP ARG ILE MET ALA
SEQRES 12 X 206 THR ILE ILE TYR LYS ASP ILE HIS CYS ASP VAL PHE PHE
SEQRES 13 X 206 PRO LEU LYS PHE ARG ASP LYS GLU TRP SER SER VAL TRP
SEQRES 14 X 206 LYS LYS GLU LYS HIS SER ASP LEU GLU SER TRP VAL GLY
SEQRES 15 X 206 THR LYS VAL PRO HIS GLY LYS ILE ASN GLU ASP GLY PHE
SEQRES 16 X 206 ASP TYR GLU PHE GLU MET TRP THR ARG ASP LEU
HET D2O X 207 31
HET PO4 X 208 5
HET GOL X 209 14
HET GOL X 210 14
HETNAM D2O 6-[2-METHOXY-5-(2-PHENYLETHOXY)BENZYL]-5-
HETNAM 2 D2O METHYLPYRIDO[2,3-D]PYRIMIDINE-2,4-DIAMINE
HETNAM PO4 PHOSPHATE ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 D2O C24 H25 N5 O2
FORMUL 3 PO4 O4 P 3-
FORMUL 4 GOL 2(C3 H8 O3)
FORMUL 6 HOH *48(H2 O)
HELIX 1 1 LEU X 29 PHE X 42 1 14
HELIX 2 2 PRO X 44 SER X 48 5 5
HELIX 3 3 ARG X 59 ILE X 65 1 7
HELIX 4 4 PRO X 66 ARG X 70 5 5
HELIX 5 5 SER X 97 TYR X 109 1 13
HELIX 6 6 GLY X 125 ASP X 134 1 10
HELIX 7 7 ASP X 162 SER X 166 5 5
HELIX 8 8 LYS X 173 GLY X 182 1 10
SHEET 1 A 8 HIS X 93 ALA X 95 0
SHEET 2 A 8 ILE X 76 ILE X 80 1 N VAL X 79 O HIS X 93
SHEET 3 A 8 SER X 51 GLY X 58 1 N ASN X 53 O ILE X 76
SHEET 4 A 8 GLN X 116 GLY X 124 1 O ASN X 118 N MET X 52
SHEET 5 A 8 LEU X 7 THR X 14 1 N ILE X 10 O VAL X 122
SHEET 6 A 8 LEU X 138 ILE X 146 1 O MET X 142 N LEU X 9
SHEET 7 A 8 PHE X 195 THR X 203 -1 O GLU X 200 N ALA X 143
SHEET 8 A 8 LYS X 170 LYS X 171 -1 N LYS X 170 O THR X 203
SHEET 1 B 8 HIS X 93 ALA X 95 0
SHEET 2 B 8 ILE X 76 ILE X 80 1 N VAL X 79 O HIS X 93
SHEET 3 B 8 SER X 51 GLY X 58 1 N ASN X 53 O ILE X 76
SHEET 4 B 8 GLN X 116 GLY X 124 1 O ASN X 118 N MET X 52
SHEET 5 B 8 LEU X 7 THR X 14 1 N ILE X 10 O VAL X 122
SHEET 6 B 8 LEU X 138 ILE X 146 1 O MET X 142 N LEU X 9
SHEET 7 B 8 PHE X 195 THR X 203 -1 O GLU X 200 N ALA X 143
SHEET 8 B 8 ILE X 190 GLU X 192 -1 N GLU X 192 O PHE X 195
SHEET 1 C 2 GLY X 18 GLY X 20 0
SHEET 2 C 2 VAL X 154 PHE X 155 -1 O VAL X 154 N ILE X 19
CISPEP 1 ARG X 70 PRO X 71 0 -6.90
CISPEP 2 SER X 85 LEU X 86 0 17.03
CISPEP 3 LEU X 88 GLY X 89 0 -14.89
SITE 1 AC1 14 ILE X 10 VAL X 11 ALA X 12 LEU X 25
SITE 2 AC1 14 GLU X 32 ILE X 33 PHE X 36 SER X 64
SITE 3 AC1 14 PRO X 66 PHE X 69 ILE X 123 TYR X 129
SITE 4 AC1 14 GOL X 210 HOH X 249
SITE 1 AC2 7 GLY X 58 LYS X 60 THR X 61 GLY X 124
SITE 2 AC2 7 GLY X 125 ALA X 126 GLN X 127
SITE 1 AC3 6 ARG X 107 SER X 166 TRP X 169 LYS X 170
SITE 2 AC3 6 LYS X 171 HOH X 227
SITE 1 AC4 5 ALA X 12 ILE X 19 LEU X 25 ILE X 123
SITE 2 AC4 5 TYR X 129
CRYST1 36.859 42.667 59.936 90.00 94.77 90.00 P 1 21 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 0.027130 0.000000 0.002264 0.00000
SCALE2 0.000000 0.023437 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016742 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
