HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 16-JUL-10 3NZ6 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]PYRIMIDINE DERIVATIVES CAVEAT 3NZ6 C-N BOND DISTANCES BETWEEN RESIDUES ASN 83 AND GLU 84 AND CAVEAT 2 3NZ6 BETWEEN RESIDUES GLY 89 AND ASN 90 ARE OUTSIDE OF THE CAVEAT 3 3NZ6 ACCEPTED RANGE FOR THE PEPTIDE BOND THE STEREOCHEMISTRY AT CAVEAT 4 3NZ6 C2'SUGAR (C13) ATOM FOR LIGAND NDP IS INCORRECT. 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: D3-157 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 3NZ6 1 REMARK REVDAT 3 08-NOV-17 3NZ6 1 REMARK REVDAT 2 12-JAN-11 3NZ6 1 DBREF JRNL SOURCE REVDAT 1 29-DEC-10 3NZ6 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) : 32.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 11724 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) : 0.208 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 619 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) : 896 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3390 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 : 79 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.02000 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): 0.238 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.156 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1769 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2396 ; 2.118 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 198 ; 8.009 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;35.794 ;23.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 311 ;20.276 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.142 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 256 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1298 ; 0.009 ; 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): 995 ; 1.113 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1616 ; 1.968 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 774 ; 2.737 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 780 ; 4.327 ; 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 3NZ6 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_1000060462. 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 : 17172 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 32.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : 0.58000 REMARK 200 FOR SHELL : 0.490 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 (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33-36% PEG 2K, 46-52 MM MES PH 6 100 REMARK 280 MM KCL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273K, PH 6.0 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 21.38400 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 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 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 GLY X 89 N ASN X 90 1.12 REMARK 500 O LEU X 88 OD1 ASN X 90 1.15 REMARK 500 C GLY X 89 CA ASN X 90 1.76 REMARK 500 N LEU X 86 O HOH X 346 1.92 REMARK 500 O ARG X 21 OD2 ASP X 153 1.99 REMARK 500 CB ASP X 87 O HOH X 357 2.07 REMARK 500 C LEU X 88 O HOH X 357 2.07 REMARK 500 O LEU X 88 O HOH X 357 2.09 REMARK 500 O LEU X 88 CG ASN X 90 2.10 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 X 221 O HOH X 267 1545 2.19 REMARK 500 O HOH X 243 O HOH X 338 1455 2.19 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 ASN X 83 C GLU X 84 N -0.469 REMARK 500 GLY X 89 C ASN X 90 N -0.893 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 ASN X 83 CA - C - N ANGL. DEV. = -36.2 DEGREES REMARK 500 ASN X 83 O - C - N ANGL. DEV. = -81.2 DEGREES REMARK 500 GLU X 84 C - N - CA ANGL. DEV. = -36.5 DEGREES REMARK 500 LEU X 88 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 GLY X 89 CA - C - N ANGL. DEV. = 41.1 DEGREES REMARK 500 GLY X 89 O - C - N ANGL. DEV. = -57.3 DEGREES REMARK 500 ARG X 107 NE - CZ - NH1 ANGL. DEV. = -3.6 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 -15.85 175.15 REMARK 500 GLN X 4 -71.32 -51.81 REMARK 500 ARG X 21 -65.55 -134.56 REMARK 500 ASN X 23 37.37 38.10 REMARK 500 PRO X 26 4.69 -68.43 REMARK 500 ASN X 83 161.66 -43.30 REMARK 500 GLU X 84 74.77 -117.86 REMARK 500 SER X 85 150.92 -49.65 REMARK 500 LEU X 86 -32.14 66.86 REMARK 500 ASP X 87 -34.73 -11.95 REMARK 500 LEU X 88 101.26 91.87 REMARK 500 ASN X 90 10.90 147.26 REMARK 500 TYR X 109 61.01 -114.58 REMARK 500 SER X 111 -42.75 -22.22 REMARK 500 SER X 113 150.52 -37.90 REMARK 500 ASN X 118 -79.27 -98.68 REMARK 500 ASP X 193 52.35 38.16 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 ASP X 87 LEU X 88 -142.99 REMARK 500 GLY X 89 ASN X 90 -128.95 REMARK 500 GLY X 124 GLY X 125 -135.24 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 ASN X 83 15.45 REMARK 500 GLY X 89 -69.75 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 D2J X 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP X 208 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: 3NZC 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 3NZ6 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 D2J X 207 31 HET NDP X 208 48 HETNAM D2J 6-{3-[(2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDIN-6- HETNAM 2 D2J YL)METHYL]-4-METHOXYPHENOXY}HEXANOIC ACID HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 2 D2J C22 H27 N5 O4 FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 HOH *166(H2 O) HELIX 1 1 LEU X 29 PHE X 42 1 14 HELIX 2 2 ARG X 59 SER X 64 1 6 HELIX 3 3 PRO X 66 ARG X 70 5 5 HELIX 4 4 SER X 97 TYR X 109 1 13 HELIX 5 5 GLY X 125 HIS X 135 1 11 HELIX 6 6 ASP X 162 SER X 166 5 5 HELIX 7 7 LYS X 173 VAL X 181 1 9 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 MET X 57 O ILE X 80 SHEET 4 A 8 GLN X 116 GLY X 124 1 O GLN X 116 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 ARG X 140 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 MET X 57 O ILE X 80 SHEET 4 B 8 GLN X 116 GLY X 124 1 O GLN X 116 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 ARG X 140 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 ILE X 190 O TYR X 197 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 -6.11 CISPEP 2 SER X 85 LEU X 86 0 5.64 SITE 1 AC1 15 ILE X 10 VAL X 11 ALA X 12 LEU X 25 SITE 2 AC1 15 GLU X 32 ILE X 33 PHE X 36 LYS X 37 SITE 3 AC1 15 SER X 64 PRO X 66 PHE X 69 ARG X 75 SITE 4 AC1 15 ILE X 123 TYR X 129 NDP X 208 SITE 1 AC2 30 VAL X 11 ALA X 12 ILE X 19 GLY X 20 SITE 2 AC2 30 ASN X 23 SER X 24 LEU X 25 TRP X 27 SITE 3 AC2 30 GLY X 58 ARG X 59 LYS X 60 THR X 61 SITE 4 AC2 30 SER X 64 ILE X 80 THR X 81 ARG X 82 SITE 5 AC2 30 LYS X 96 ILE X 123 GLY X 125 ALA X 126 SITE 6 AC2 30 GLN X 127 LEU X 128 TYR X 129 ALA X 131 SITE 7 AC2 30 D2J X 207 HOH X 213 HOH X 231 HOH X 262 SITE 8 AC2 30 HOH X 340 HOH X 353 CRYST1 37.113 42.768 60.756 90.00 94.39 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 0.026945 0.000000 0.002069 0.00000 SCALE2 0.000000 0.023382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016508 0.00000