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 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 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 TER 1687 LEU X 206 HETATM 1688 N1 D2O X 207 10.339 -1.850 13.066 0.50 20.79 N HETATM 1689 C2 D2O X 207 10.604 -2.674 12.059 0.50 17.78 C HETATM 1690 N3 D2O X 207 11.541 -2.362 11.199 0.50 23.43 N HETATM 1691 C4 D2O X 207 12.238 -1.248 11.316 0.50 24.76 C HETATM 1692 C5 D2O X 207 11.987 -0.366 12.350 0.50 21.56 C HETATM 1693 C6 D2O X 207 10.984 -0.714 13.248 0.50 19.19 C HETATM 1694 CAA D2O X 207 18.483 1.446 12.037 0.50 43.36 C HETATM 1695 CAB D2O X 207 12.648 1.896 13.409 0.50 14.42 C HETATM 1696 NAC D2O X 207 9.935 -3.800 11.891 0.50 17.45 N HETATM 1697 NAD D2O X 207 10.644 0.019 14.269 0.50 14.10 N HETATM 1698 CAE D2O X 207 15.938 1.757 2.184 0.50 45.18 C HETATM 1699 CAF D2O X 207 16.832 1.796 3.241 0.50 43.88 C HETATM 1700 CAG D2O X 207 14.867 2.641 2.107 0.50 45.33 C HETATM 1701 CAH D2O X 207 16.622 2.748 4.230 0.50 43.72 C HETATM 1702 CAI D2O X 207 14.672 3.579 3.097 0.50 44.91 C HETATM 1703 CAJ D2O X 207 17.643 2.643 8.576 0.50 42.41 C HETATM 1704 CAK D2O X 207 17.914 2.195 9.850 0.50 42.10 C HETATM 1705 CAL D2O X 207 13.896 0.110 10.436 0.50 30.23 C HETATM 1706 CAM D2O X 207 15.334 2.919 9.134 0.50 41.54 C HETATM 1707 CAN D2O X 207 14.962 4.047 6.639 0.50 45.39 C HETATM 1708 CAO D2O X 207 15.325 4.679 5.290 0.50 44.24 C HETATM 1709 CAP D2O X 207 14.529 2.337 11.490 0.50 34.71 C HETATM 1710 NAQ D2O X 207 13.173 -0.994 10.408 0.50 29.24 N HETATM 1711 OAT D2O X 207 17.107 1.674 12.015 0.50 44.67 O HETATM 1712 OAU D2O X 207 16.173 3.444 6.972 0.50 46.43 O HETATM 1713 CAV D2O X 207 15.548 3.636 4.167 0.50 44.33 C HETATM 1714 CAW D2O X 207 16.365 3.017 8.220 0.50 43.51 C HETATM 1715 CAY D2O X 207 13.712 1.057 11.431 0.50 27.25 C HETATM 1716 CAZ D2O X 207 15.611 2.443 10.423 0.50 39.93 C HETATM 1717 CBB D2O X 207 12.756 0.810 12.384 0.50 22.59 C HETATM 1718 CBC D2O X 207 16.891 2.098 10.761 0.50 41.62 C HETATM 1719 P PO4 X 208 15.495 4.401 22.937 1.00 30.00 P HETATM 1720 O1 PO4 X 208 16.810 4.979 22.210 1.00 30.00 O HETATM 1721 O2 PO4 X 208 14.180 4.979 22.210 1.00 30.00 O HETATM 1722 O3 PO4 X 208 15.495 2.793 22.846 1.00 30.00 O HETATM 1723 O4 PO4 X 208 15.495 4.814 24.358 1.00 30.00 O HETATM 1724 C1 GOL X 209 -2.995 -15.580 20.091 1.00 20.00 C HETATM 1725 O1 GOL X 209 -2.118 -16.138 19.203 1.00 20.00 O HETATM 1726 C2 GOL X 209 -2.756 -16.013 21.544 1.00 20.00 C HETATM 1727 O2 GOL X 209 -1.558 -15.622 22.002 1.00 20.00 O HETATM 1728 C3 GOL X 209 -2.975 -17.503 21.697 1.00 20.00 C HETATM 1729 O3 GOL X 209 -3.917 -17.751 22.671 1.00 20.00 O HETATM 1730 H11 GOL X 209 -2.924 -14.497 20.021 1.00 20.00 H HETATM 1731 H12 GOL X 209 -4.004 -15.860 19.791 1.00 20.00 H HETATM 1732 HO1 GOL X 209 -1.219 -16.093 19.570 1.00 20.00 H HETATM 1733 H2 GOL X 209 -3.517 -15.519 22.145 1.00 20.00 H HETATM 1734 HO2 GOL X 209 -1.395 -16.001 22.883 1.00 20.00 H HETATM 1735 H31 GOL X 209 -3.333 -17.900 20.746 1.00 20.00 H HETATM 1736 H32 GOL X 209 -2.037 -17.995 21.938 1.00 20.00 H HETATM 1737 HO3 GOL X 209 -4.056 -18.713 22.771 1.00 20.00 H HETATM 1738 C1 GOL X 210 13.457 -0.217 16.183 1.00 20.00 C HETATM 1739 O1 GOL X 210 14.459 0.575 16.747 1.00 20.00 O HETATM 1740 C2 GOL X 210 13.548 -1.596 16.794 1.00 20.00 C HETATM 1741 O2 GOL X 210 14.899 -1.789 17.126 1.00 20.00 O HETATM 1742 C3 GOL X 210 13.156 -2.751 15.873 1.00 20.00 C HETATM 1743 O3 GOL X 210 14.321 -3.516 15.646 1.00 20.00 O HETATM 1744 H11 GOL X 210 12.486 0.232 16.382 1.00 20.00 H HETATM 1745 H12 GOL X 210 13.600 -0.258 15.109 1.00 20.00 H HETATM 1746 HO1 GOL X 210 14.418 1.478 16.376 1.00 20.00 H HETATM 1747 H2 GOL X 210 12.920 -1.611 17.687 1.00 20.00 H HETATM 1748 HO2 GOL X 210 15.178 -1.269 17.914 1.00 20.00 H HETATM 1749 H31 GOL X 210 12.389 -3.378 16.320 1.00 20.00 H HETATM 1750 H32 GOL X 210 12.759 -2.389 14.932 1.00 20.00 H HETATM 1751 HO3 GOL X 210 14.605 -3.971 16.464 1.00 20.00 H HETATM 1752 O HOH X 211 7.814 -10.919 29.747 1.00 35.00 O HETATM 1753 O HOH X 212 4.241 -6.477 11.025 1.00 28.43 O HETATM 1754 O HOH X 213 -1.815 3.390 15.430 1.00 34.23 O HETATM 1755 O HOH X 214 1.447 -14.554 23.671 1.00 25.69 O HETATM 1756 O HOH X 215 -1.491 -13.826 29.394 1.00 28.96 O HETATM 1757 O HOH X 216 -0.358 -11.824 11.947 1.00 28.77 O HETATM 1758 O HOH X 217 5.447 -12.876 6.120 1.00 32.82 O HETATM 1759 O HOH X 218 -3.088 5.403 16.241 1.00 41.91 O HETATM 1760 O HOH X 219 7.675 17.494 26.858 1.00 36.47 O HETATM 1761 O HOH X 220 6.686 -5.347 11.799 1.00 32.44 O HETATM 1762 O HOH X 221 -0.721 2.743 8.475 1.00 34.90 O HETATM 1763 O HOH X 222 -7.475 -11.974 13.045 1.00 41.91 O HETATM 1764 O HOH X 223 18.543 -13.045 19.125 1.00 29.07 O HETATM 1765 O HOH X 224 7.213 7.808 28.105 1.00 40.17 O HETATM 1766 O HOH X 225 29.940 -9.571 21.646 1.00 47.07 O HETATM 1767 O HOH X 226 -6.450 -8.833 25.379 1.00 34.49 O HETATM 1768 O HOH X 227 0.844 -16.800 22.150 1.00 35.02 O HETATM 1769 O HOH X 228 -5.039 -14.975 6.274 1.00 47.77 O HETATM 1770 O HOH X 229 3.798 8.863 29.536 1.00 39.39 O HETATM 1771 O HOH X 230 -3.450 -16.206 8.829 1.00 40.91 O HETATM 1772 O HOH X 231 -1.232 -1.614 26.481 1.00 34.39 O HETATM 1773 O HOH X 232 -10.468 -1.016 29.873 1.00 50.29 O HETATM 1774 O HOH X 233 -7.692 -5.776 10.440 1.00 39.43 O HETATM 1775 O HOH X 234 2.154 -19.902 31.834 1.00 40.91 O HETATM 1776 O HOH X 235 17.095 -3.900 8.160 1.00 40.73 O HETATM 1777 O HOH X 236 -11.523 -3.920 25.801 1.00 50.35 O HETATM 1778 O HOH X 237 1.956 9.409 6.961 1.00 39.25 O HETATM 1779 O HOH X 238 13.343 13.875 5.200 1.00 47.78 O HETATM 1780 O HOH X 239 -7.624 -16.264 25.721 1.00 51.65 O HETATM 1781 O HOH X 240 3.705 4.371 29.962 1.00 47.56 O HETATM 1782 O HOH X 241 5.729 -19.744 25.413 1.00 37.53 O HETATM 1783 O HOH X 242 13.125 9.371 5.375 1.00 35.49 O HETATM 1784 O HOH X 243 0.593 -12.620 9.654 1.00 42.98 O HETATM 1785 O HOH X 244 3.146 -14.132 7.679 1.00 51.58 O HETATM 1786 O HOH X 245 5.709 -18.156 28.812 1.00 32.45 O HETATM 1787 O HOH X 246 17.657 -4.675 26.405 1.00 41.66 O HETATM 1788 O HOH X 247 7.874 19.401 23.609 1.00 42.35 O HETATM 1789 O HOH X 248 1.652 -5.035 29.748 1.00 54.96 O HETATM 1790 O HOH X 249 14.880 -0.507 2.215 1.00 55.56 O HETATM 1791 O HOH X 250 9.234 -15.261 20.186 1.00 44.49 O HETATM 1792 O HOH X 251 -3.321 18.848 23.993 1.00 46.73 O HETATM 1793 O HOH X 252 -3.815 0.224 16.834 1.00 28.80 O HETATM 1794 O HOH X 253 9.191 20.076 20.251 1.00 53.20 O HETATM 1795 O HOH X 254 3.464 18.297 26.026 1.00 37.98 O HETATM 1796 O HOH X 255 11.138 4.679 6.430 1.00 30.61 O HETATM 1797 O HOH X 256 15.021 -4.672 27.376 1.00 49.80 O HETATM 1798 O HOH X 257 -7.373 -5.881 13.600 1.00 53.74 O HETATM 1799 O HOH X 258 -5.500 5.762 14.867 1.00 47.61 O CONECT 1688 1689 1693 CONECT 1689 1688 1690 1696 CONECT 1690 1689 1691 CONECT 1691 1690 1692 1710 CONECT 1692 1691 1693 1717 CONECT 1693 1688 1692 1697 CONECT 1694 1711 CONECT 1695 1717 CONECT 1696 1689 CONECT 1697 1693 CONECT 1698 1699 1700 CONECT 1699 1698 1701 CONECT 1700 1698 1702 CONECT 1701 1699 1713 CONECT 1702 1700 1713 CONECT 1703 1704 1714 CONECT 1704 1703 1718 CONECT 1705 1710 1715 CONECT 1706 1714 1716 CONECT 1707 1708 1712 CONECT 1708 1707 1713 CONECT 1709 1715 1716 CONECT 1710 1691 1705 CONECT 1711 1694 1718 CONECT 1712 1707 1714 CONECT 1713 1701 1702 1708 CONECT 1714 1703 1706 1712 CONECT 1715 1705 1709 1717 CONECT 1716 1706 1709 1718 CONECT 1717 1692 1695 1715 CONECT 1718 1704 1711 1716 CONECT 1719 1720 1721 1722 1723 CONECT 1720 1719 CONECT 1721 1719 CONECT 1722 1719 CONECT 1723 1719 CONECT 1724 1725 1726 1730 1731 CONECT 1725 1724 1732 CONECT 1726 1724 1727 1728 1733 CONECT 1727 1726 1734 CONECT 1728 1726 1729 1735 1736 CONECT 1729 1728 1737 CONECT 1730 1724 CONECT 1731 1724 CONECT 1732 1725 CONECT 1733 1726 CONECT 1734 1727 CONECT 1735 1728 CONECT 1736 1728 CONECT 1737 1729 CONECT 1738 1739 1740 1744 1745 CONECT 1739 1738 1746 CONECT 1740 1738 1741 1742 1747 CONECT 1741 1740 1748 CONECT 1742 1740 1743 1749 1750 CONECT 1743 1742 1751 CONECT 1744 1738 CONECT 1745 1738 CONECT 1746 1739 CONECT 1747 1740 CONECT 1748 1741 CONECT 1749 1742 CONECT 1750 1742 CONECT 1751 1743 MASTER 402 0 4 8 18 0 10 6 1782 1 64 16 END