HEADER HYDROLASE 28-SEP-16 5LYF TITLE CRYSTAL STRUCTURE OF 1 IN COMPLEX WITH TAFCPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOXYPEPTIDASE B; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.17.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 GENE: CPB1, CPB; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS CBS 7435; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 981350 KEYWDS TAFINIZED CARBOXYPEPTIDASE B, HYRDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SCHREUDER,A.LIESUM,P.LOENZE REVDAT 2 21-DEC-16 5LYF 1 JRNL REVDAT 1 26-OCT-16 5LYF 0 JRNL AUTH N.HALLAND,J.CZECH,W.CZECHTIZKY,A.EVERS,M.FOLLMANN, JRNL AUTH 2 M.KOHLMANN,H.A.SCHREUDER,C.KALLUS JRNL TITL SULFAMIDE AS ZINC BINDING MOTIF IN SMALL MOLECULE INHIBITORS JRNL TITL 2 OF ACTIVATED THROMBIN ACTIVATABLE FIBRINOLYSIS INHIBITOR JRNL TITL 3 (TAFIA). JRNL REF J. MED. CHEM. V. 59 9567 2016 JRNL REFN ISSN 1520-4804 JRNL PMID 27749053 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01276 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 20300 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) : 0.184 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1522 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1354 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 582 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.25000 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): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.973 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.845 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2552 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3476 ; 1.956 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 7.252 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;33.350 ;24.034 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;16.965 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.651 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 369 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1964 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1471 ; 0.252 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1719 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 420 ; 0.267 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.057 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 42 ; 0.311 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 43 ; 0.278 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.272 ; 0.200 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): 1560 ; 1.096 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2439 ; 1.663 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1191 ; 2.591 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1037 ; 3.512 ; 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 : NULL 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 5LYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21825 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 81.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.28400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.990 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PURIFIED PROTEIN WAS DISSOLVED IN REMARK 280 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF REMARK 280 PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR REMARK 280 SOLUTIONS CONTAINING 16-20% PEG3350, 100 MM MES PH 5.5 AND 50 MM REMARK 280 ZNACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.86700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.74500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.93350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.74500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.74500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.80050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.74500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.74500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.93350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.74500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.74500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.80050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.86700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 923 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 950 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 4 REMARK 465 THR A 5 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 LEU A 230 O HOH A 501 1.99 REMARK 500 O HOH A 718 O HOH A 891 2.00 REMARK 500 O HOH A 547 O HOH A 566 2.01 REMARK 500 O HOH A 557 O HOH A 762 2.03 REMARK 500 O HOH A 593 O HOH A 926 2.04 REMARK 500 O HOH A 610 O HOH A 992 2.08 REMARK 500 O HOH A 639 O HOH A 1010 2.09 REMARK 500 O HOH A 725 O HOH A 825 2.10 REMARK 500 O HOH A 701 O HOH A 765 2.11 REMARK 500 O HOH A 570 O HOH A 700 2.11 REMARK 500 O HOH A 611 O HOH A 754 2.13 REMARK 500 O THR A 232 O HOH A 502 2.14 REMARK 500 O HOH A 717 O HOH A 786 2.14 REMARK 500 O HOH A 690 O HOH A 892 2.16 REMARK 500 O HOH A 795 O HOH A 804 2.16 REMARK 500 OE1 GLU A 171 O HOH A 503 2.18 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 ZN ZN A 403 ZN ZN A 403 8666 1.09 REMARK 500 O HOH A 559 O HOH A 706 5656 2.14 REMARK 500 O HOH A 505 O HOH A 640 3645 2.18 REMARK 500 CG2 THR A 245 O HOH A 706 5656 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 CYS A 66 CB CYS A 66 SG 0.118 REMARK 500 GLU A 72 CD GLU A 72 OE1 0.080 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 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 PRO A 242 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 LEU A 247 CA - CB - CG ANGL. DEV. = 13.9 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 LYS A 122 -42.13 -132.76 REMARK 500 THR A 153 -165.53 -102.16 REMARK 500 TYR A 198 -169.37 -117.06 REMARK 500 SER A 199 1.09 126.01 REMARK 500 ASN A 215 38.44 -95.57 REMARK 500 ALA A 231 1.45 -68.53 REMARK 500 LEU A 247 -92.10 -92.16 REMARK 500 ALA A 250 67.69 -156.82 REMARK 500 ASP A 273 -143.04 -116.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1060 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1061 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1062 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1063 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A1064 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1065 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A1066 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1067 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1068 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A1069 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A1070 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1071 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH A1072 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A1073 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A1074 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A1075 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH A1076 DISTANCE = 7.34 ANGSTROMS REMARK 525 HOH A1077 DISTANCE = 8.06 ANGSTROMS REMARK 525 HOH A1078 DISTANCE = 8.12 ANGSTROMS REMARK 525 HOH A1079 DISTANCE = 8.22 ANGSTROMS REMARK 525 HOH A1080 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH A1081 DISTANCE = 8.85 ANGSTROMS REMARK 525 HOH A1082 DISTANCE = 9.55 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 ND1 REMARK 620 2 GLU A 72 OE1 118.3 REMARK 620 3 GLU A 72 OE2 92.5 62.2 REMARK 620 4 HIS A 196 ND1 101.3 99.7 161.2 REMARK 620 5 HOH A 552 O 122.2 106.2 76.8 105.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 85 OE2 REMARK 620 2 GLU A 291 OE1 82.6 REMARK 620 3 GLU A 291 OE2 107.4 56.5 REMARK 620 4 HOH A 576 O 93.3 159.2 106.2 REMARK 620 5 ASP A 159 OD1 44.1 49.3 64.8 115.2 REMARK 620 6 ASP A 162 OD2 45.9 48.3 63.0 115.7 1.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 307 NE2 REMARK 620 2 HIS A 307 NE2 0.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7B6 A 404 DBREF 5LYF A 4 308 UNP P09955 CBPB1_PIG 111 416 SEQADV 5LYF ILE A 68 UNP P09955 PHE 175 CONFLICT SEQADV 5LYF SER A 194 UNP P09955 THR 302 CONFLICT SEQADV 5LYF HIS A 201 UNP P09955 MET 309 CONFLICT SEQADV 5LYF VAL A 203 UNP P09955 LEU 311 CONFLICT SEQADV 5LYF LEU A 247 UNP P09955 ILE 355 CONFLICT SEQADV 5LYF LEU A 249 UNP P09955 PRO 357 CONFLICT SEQADV 5LYF PRO A 251 UNP P09955 ALA 359 CONFLICT SEQADV 5LYF GLY A 254 UNP P09955 SER 362 CONFLICT SEQADV 5LYF TYR A 309 UNP P09955 EXPRESSION TAG SEQRES 1 A 307 THR THR GLY HIS SER TYR GLU LYS TYR ASN ASN TRP GLU SEQRES 2 A 307 THR ILE GLU ALA TRP THR LYS GLN VAL THR SER GLU ASN SEQRES 3 A 307 PRO ASP LEU ILE SER ARG THR ALA ILE GLY THR THR PHE SEQRES 4 A 307 LEU GLY ASN ASN ILE TYR LEU LEU LYS VAL GLY LYS PRO SEQRES 5 A 307 GLY PRO ASN LYS PRO ALA ILE PHE MET ASP CYS GLY ILE SEQRES 6 A 307 HIS ALA ARG GLU TRP ILE SER HIS ALA PHE CYS GLN TRP SEQRES 7 A 307 PHE VAL ARG GLU ALA VAL LEU THR TYR GLY TYR GLU SER SEQRES 8 A 307 HIS MET THR GLU PHE LEU ASN LYS LEU ASP PHE TYR VAL SEQRES 9 A 307 LEU PRO VAL LEU ASN ILE ASP GLY TYR ILE TYR THR TRP SEQRES 10 A 307 THR LYS ASN ARG MET TRP ARG LYS THR ARG SER THR ASN SEQRES 11 A 307 ALA GLY THR THR CYS ILE GLY THR ASP PRO ASN ARG ASN SEQRES 12 A 307 PHE ASP ALA GLY TRP CYS THR THR GLY ALA SER THR ASP SEQRES 13 A 307 PRO CYS ASP GLU THR TYR CYS GLY SER ALA ALA GLU SER SEQRES 14 A 307 GLU LYS GLU THR LYS ALA LEU ALA ASP PHE ILE ARG ASN SEQRES 15 A 307 ASN LEU SER SER ILE LYS ALA TYR LEU SER ILE HIS SER SEQRES 16 A 307 TYR SER GLN HIS ILE VAL TYR PRO TYR SER TYR ASP TYR SEQRES 17 A 307 LYS LEU PRO GLU ASN ASN ALA GLU LEU ASN ASN LEU ALA SEQRES 18 A 307 LYS ALA ALA VAL LYS GLU LEU ALA THR LEU TYR GLY THR SEQRES 19 A 307 LYS TYR THR TYR GLY PRO GLY ALA THR THR LEU TYR LEU SEQRES 20 A 307 ALA PRO GLY GLY GLY ASP ASP TRP ALA TYR ASP GLN GLY SEQRES 21 A 307 ILE LYS TYR SER PHE THR PHE GLU LEU ARG ASP LYS GLY SEQRES 22 A 307 ARG TYR GLY PHE ILE LEU PRO GLU SER GLN ILE GLN ALA SEQRES 23 A 307 THR CYS GLU GLU THR MET LEU ALA ILE LYS TYR VAL THR SEQRES 24 A 307 ASN TYR VAL LEU GLY HIS LEU TYR HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HET 7B6 A 404 31 HETNAM ZN ZINC ION HETNAM 7B6 (2~{S})-6-AZANYL-2-[[(2~{R})-1-[[(1~{R},2~{S},4~{S})-2- HETNAM 2 7B6 BICYCLO[2.2.1]HEPTANYL]AMINO]-3-CYCLOHEXYL-1- HETNAM 3 7B6 OXIDANYLIDENE-PROPAN-2-YL]CARBAMOYLAMINO]HEXANOIC ACID FORMUL 2 ZN 3(ZN 2+) FORMUL 5 7B6 C23 H40 N4 O4 FORMUL 6 HOH *582(H2 O) HELIX 1 AA1 ASN A 14 ASN A 29 1 16 HELIX 2 AA2 GLU A 72 TYR A 90 1 19 HELIX 3 AA3 GLU A 93 LEU A 103 1 11 HELIX 4 AA4 ASN A 112 LYS A 122 1 11 HELIX 5 AA5 ASP A 142 ASN A 146 5 5 HELIX 6 AA6 GLU A 173 ASN A 186 1 14 HELIX 7 AA7 ASN A 215 ALA A 231 1 17 HELIX 8 AA8 GLY A 243 LEU A 247 1 5 HELIX 9 AA9 GLY A 253 GLN A 261 1 9 HELIX 10 AB1 PRO A 282 SER A 284 5 3 HELIX 11 AB2 GLN A 285 HIS A 307 1 23 SHEET 1 AA1 8 ILE A 33 THR A 40 0 SHEET 2 AA1 8 ASN A 46 VAL A 52 -1 O ILE A 47 N ILE A 38 SHEET 3 AA1 8 ASP A 104 LEU A 108 -1 O VAL A 107 N LEU A 50 SHEET 4 AA1 8 ALA A 61 CYS A 66 1 N MET A 64 O TYR A 106 SHEET 5 AA1 8 ILE A 189 HIS A 196 1 O LYS A 190 N ALA A 61 SHEET 6 AA1 8 TYR A 265 GLU A 270 1 O PHE A 269 N HIS A 196 SHEET 7 AA1 8 HIS A 201 TYR A 204 -1 N VAL A 203 O THR A 268 SHEET 8 AA1 8 THR A 239 PRO A 242 1 O THR A 239 N ILE A 202 SSBOND 1 CYS A 66 CYS A 79 1555 1555 2.04 SSBOND 2 CYS A 138 CYS A 161 1555 1555 2.02 SSBOND 3 CYS A 152 CYS A 166 1555 1555 2.03 LINK ND1 HIS A 69 ZN ZN A 401 1555 1555 2.06 LINK OE1 GLU A 72 ZN ZN A 401 1555 1555 2.11 LINK OE2 GLU A 72 ZN ZN A 401 1555 1555 2.41 LINK OE2 GLU A 85 ZN ZN A 402 1555 1555 2.41 LINK ND1 HIS A 196 ZN ZN A 401 1555 1555 2.21 LINK OE1 GLU A 291 ZN ZN A 402 1555 1555 2.33 LINK OE2 GLU A 291 ZN ZN A 402 1555 1555 2.25 LINK NE2 HIS A 307 ZN ZN A 403 1555 1555 2.35 LINK ZN ZN A 401 O HOH A 552 1555 1555 1.96 LINK ZN ZN A 402 O HOH A 576 1555 1555 2.34 LINK OD1 ASP A 159 ZN ZN A 402 1555 4564 1.99 LINK OD2 ASP A 162 ZN ZN A 402 1555 4564 2.11 LINK NE2 HIS A 307 ZN ZN A 403 1555 8666 2.33 CISPEP 1 SER A 197 TYR A 198 0 -9.67 CISPEP 2 PRO A 205 TYR A 206 0 12.64 CISPEP 3 ARG A 272 ASP A 273 0 -4.90 SITE 1 AC1 5 HIS A 69 GLU A 72 HIS A 196 7B6 A 404 SITE 2 AC1 5 HOH A 552 SITE 1 AC2 5 GLU A 85 ASP A 159 ASP A 162 GLU A 291 SITE 2 AC2 5 HOH A 576 SITE 1 AC3 1 HIS A 307 SITE 1 AC4 20 HIS A 69 ARG A 71 ARG A 127 ASN A 144 SITE 2 AC4 20 ARG A 145 SER A 197 TYR A 198 SER A 207 SITE 3 AC4 20 TYR A 248 ASP A 255 GLU A 270 PHE A 279 SITE 4 AC4 20 ZN A 401 HOH A 502 HOH A 552 HOH A 555 SITE 5 AC4 20 HOH A 605 HOH A 630 HOH A 640 HOH A 885 CRYST1 81.490 81.490 95.734 90.00 90.00 90.00 P 41 21 2 8 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 0.012271 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010446 0.00000