HEADER HYDROLASE 10-NOV-15 5EOK TITLE HUMAN PLASMA COAGULATION FACTOR XI IN COMPLEX WITH PEPTIDE P39 CAVEAT 5EOK GLU A 323 HAS WRONG CHIRALITY AT ATOM CA NAG B 2 HAS WRONG CAVEAT 2 5EOK CHIRALITY AT ATOM C1 NAG A 701 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 5EOK C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR XI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-265; COMPND 5 SYNONYM: FXI,PLASMA THROMBOPLASTIN ANTECEDENT,PTA; COMPND 6 EC: 3.4.21.27; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: P39; COMPND 10 CHAIN: K; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F11; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS HUMAN, PLASMA, COAGULATION FXI, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.S.WONG,S.OSTERGAARD,G.HALL,C.LI,P.M.WILLIAMS,H.STENNICKE,J.EMSLEY REVDAT 3 29-JUL-20 5EOK 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 SSBOND LINK SITE ATOM REVDAT 2 22-JUN-16 5EOK 1 JRNL REVDAT 1 06-APR-16 5EOK 0 JRNL AUTH S.S.WONG,S.STERGAARD,G.HALL,C.LI,P.M.WILLIAMS,H.STENNICKE, JRNL AUTH 2 J.EMSLEY JRNL TITL A NOVEL DFP TRIPEPTIDE MOTIF INTERACTS WITH THE COAGULATION JRNL TITL 2 FACTOR XI APPLE 2 DOMAIN. JRNL REF BLOOD V. 127 2915 2016 JRNL REFN ESSN 1528-0020 JRNL PMID 27006387 JRNL DOI 10.1182/BLOOD-2015-10-676122 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 19639 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1065 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 952 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.3930 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.4440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4703 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60000 REMARK 3 B22 (A**2) : -0.60000 REMARK 3 B33 (A**2) : 1.19000 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): 1.332 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.374 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.286 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.802 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4810 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6527 ; 1.762 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 575 ; 7.247 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;36.815 ;23.768 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 791 ;21.848 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 736 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3570 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5EOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20795 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5, 20% PEG1500, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 126.10950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.66500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 189.16425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.66500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.66500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.05475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.66500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.66500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 189.16425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.66500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.66500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.05475 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 126.10950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, K, B 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 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 ARG A 504 REMARK 465 LYS A 505 REMARK 465 LEU A 506 REMARK 465 ARG A 507 REMARK 465 ARG A 546 REMARK 465 GLU A 547 REMARK 465 GLY A 548 REMARK 465 GLY A 549 REMARK 465 LYS A 550 REMARK 465 ASP A 551 REMARK 465 ALA A 552 REMARK 465 CYS A 553 REMARK 465 ALA A 582 REMARK 465 GLN A 583 REMARK 465 ARG A 584 REMARK 465 ALA A 606 REMARK 465 VAL A 607 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 GLN A 318 REMARK 475 ALA A 319 REMARK 475 SER A 320 REMARK 475 CYS A 321 REMARK 475 GLY A 324 REMARK 475 LYS A 367 REMARK 475 PRO A 368 REMARK 475 ARG A 369 REMARK 475 ILE A 370 REMARK 475 VAL A 371 REMARK 475 GLY A 372 REMARK 475 GLY A 373 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 78 C O CB OG REMARK 480 LYS A 253 C O CD CE NZ REMARK 480 LYS A 294 C O CD CE NZ REMARK 480 GLU A 323 C O CG CD OE1 OE2 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 CYS A 321 N ASN A 322 1.64 REMARK 500 O ALA A 317 N GLN A 318 1.70 REMARK 500 O ILE A 366 N LYS A 367 1.77 REMARK 500 CA LYS A 253 N SER A 254 1.79 REMARK 500 OG1 THR A 42 OG SER A 78 2.04 REMARK 500 O GLU A 323 N LYS A 325 2.13 REMARK 500 OH TYR A 107 OD1 ASP A 125 2.16 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 SER A 78 CA SER A 78 CB -0.163 REMARK 500 SER A 78 CA SER A 78 C -0.165 REMARK 500 SER A 78 C GLY A 79 N -0.203 REMARK 500 LYS A 252 C LYS A 253 N 0.146 REMARK 500 LYS A 253 CA LYS A 253 CB 0.182 REMARK 500 LYS A 253 CG LYS A 253 CD -0.315 REMARK 500 LYS A 253 CA LYS A 253 C -0.280 REMARK 500 LYS A 253 C SER A 254 N -0.277 REMARK 500 LYS A 294 CA LYS A 294 C -0.158 REMARK 500 LYS A 294 C SER A 295 N -0.202 REMARK 500 ALA A 317 C GLN A 318 N -0.273 REMARK 500 CYS A 321 C ASN A 322 N -0.516 REMARK 500 GLU A 323 CA GLU A 323 CB 0.135 REMARK 500 GLU A 323 CB GLU A 323 CG -0.162 REMARK 500 GLU A 323 CA GLU A 323 C -0.422 REMARK 500 GLY A 324 C LYS A 325 N 0.199 REMARK 500 ILE A 366 C LYS A 367 N -0.271 REMARK 500 GLY A 373 C THR A 374 N -0.149 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 SER A 78 CB - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 SER A 78 CA - C - N ANGL. DEV. = 12.8 DEGREES REMARK 500 LYS A 253 CB - CA - C ANGL. DEV. = -21.4 DEGREES REMARK 500 LYS A 253 CA - C - N ANGL. DEV. = -15.7 DEGREES REMARK 500 LYS A 294 CB - CG - CD ANGL. DEV. = 18.3 DEGREES REMARK 500 ALA A 317 CA - C - N ANGL. DEV. = 19.1 DEGREES REMARK 500 ALA A 317 O - C - N ANGL. DEV. = -30.9 DEGREES REMARK 500 GLN A 318 C - N - CA ANGL. DEV. = 21.2 DEGREES REMARK 500 CYS A 321 CA - C - N ANGL. DEV. = 14.0 DEGREES REMARK 500 CYS A 321 O - C - N ANGL. DEV. = -21.3 DEGREES REMARK 500 ASN A 322 C - N - CA ANGL. DEV. = 23.7 DEGREES REMARK 500 ASN A 322 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 GLU A 323 CB - CA - C ANGL. DEV. = 34.1 DEGREES REMARK 500 GLU A 323 CA - CB - CG ANGL. DEV. = 21.3 DEGREES REMARK 500 GLY A 324 CA - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 GLY A 324 O - C - N ANGL. DEV. = 10.3 DEGREES REMARK 500 LYS A 325 C - N - CA ANGL. DEV. = -19.6 DEGREES REMARK 500 ILE A 366 CA - C - N ANGL. DEV. = 18.1 DEGREES REMARK 500 ILE A 366 O - C - N ANGL. DEV. = -24.9 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 VAL A 3 86.76 -69.62 REMARK 500 ASP A 9 50.82 -142.81 REMARK 500 SER A 24 145.55 -174.79 REMARK 500 PRO A 48 -36.92 -39.94 REMARK 500 PRO A 52 -39.31 -38.25 REMARK 500 ASP A 99 17.52 54.74 REMARK 500 SER A 140 107.46 -53.11 REMARK 500 ALA A 176 43.43 -75.56 REMARK 500 ASP A 194 172.35 176.74 REMARK 500 ASN A 235 12.62 59.78 REMARK 500 LYS A 253 161.49 158.85 REMARK 500 CYS A 265 30.85 -91.52 REMARK 500 SER A 268 -4.67 63.78 REMARK 500 VAL A 271 -64.94 -137.61 REMARK 500 ALA A 317 66.19 -64.37 REMARK 500 GLN A 318 144.78 -39.25 REMARK 500 ALA A 319 -129.20 61.28 REMARK 500 ARG A 354 -29.13 -36.17 REMARK 500 PRO A 382 4.97 -68.86 REMARK 500 HIS A 413 -12.30 -45.25 REMARK 500 LEU A 431 -78.18 -127.99 REMARK 500 SER A 434 0.08 -63.25 REMARK 500 LYS A 455 -73.18 -141.23 REMARK 500 THR A 494 14.59 -146.93 REMARK 500 LYS A 509 108.57 -162.05 REMARK 500 ILE A 541 145.66 -173.41 REMARK 500 GLU A 567 -5.37 75.72 REMARK 500 SER A 576 -64.94 -120.16 REMARK 500 ASP K 2 -174.63 -67.42 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 ALA A 317 GLN A 318 -147.60 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 LYS A 253 13.87 REMARK 500 ALA A 317 35.42 REMARK 500 CYS A 321 10.37 REMARK 500 ILE A 366 25.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EOK A 2 607 UNP P03951 FA11_HUMAN 20 625 DBREF 5EOK K -2 6 PDB 5EOK 5EOK -2 6 SEQRES 1 A 606 CYS VAL THR GLN LEU LEU LYS ASP THR CYS PHE GLU GLY SEQRES 2 A 606 GLY ASP ILE THR THR VAL PHE THR PRO SER ALA LYS TYR SEQRES 3 A 606 CYS GLN VAL VAL CYS THR TYR HIS PRO ARG CYS LEU LEU SEQRES 4 A 606 PHE THR PHE THR ALA GLU SER PRO SER GLU ASP PRO THR SEQRES 5 A 606 ARG TRP PHE THR CYS VAL LEU LYS ASP SER VAL THR GLU SEQRES 6 A 606 THR LEU PRO ARG VAL ASN ARG THR ALA ALA ILE SER GLY SEQRES 7 A 606 TYR SER PHE LYS GLN CYS SER HIS GLN ILE SER ALA CYS SEQRES 8 A 606 ASN LYS ASP ILE TYR VAL ASP LEU ASP MET LYS GLY ILE SEQRES 9 A 606 ASN TYR ASN SER SER VAL ALA LYS SER ALA GLN GLU CYS SEQRES 10 A 606 GLN GLU ARG CYS THR ASP ASP VAL HIS CYS HIS PHE PHE SEQRES 11 A 606 THR TYR ALA THR ARG GLN PHE PRO SER LEU GLU HIS ARG SEQRES 12 A 606 ASN ILE CYS LEU LEU LYS HIS THR GLN THR GLY THR PRO SEQRES 13 A 606 THR ARG ILE THR LYS LEU ASP LYS VAL VAL SER GLY PHE SEQRES 14 A 606 SER LEU LYS SER CYS ALA LEU SER ASN LEU ALA CYS ILE SEQRES 15 A 606 ARG ASP ILE PHE PRO ASN THR VAL PHE ALA ASP SER ASN SEQRES 16 A 606 ILE ASP SER VAL MET ALA PRO ASP ALA PHE VAL CYS GLY SEQRES 17 A 606 ARG ILE CYS THR HIS HIS PRO GLY CYS LEU PHE PHE THR SEQRES 18 A 606 PHE PHE SER GLN GLU TRP PRO LYS GLU SER GLN ARG ASN SEQRES 19 A 606 LEU CYS LEU LEU LYS THR SER GLU SER GLY LEU PRO SER SEQRES 20 A 606 THR ARG ILE LYS LYS SER LYS ALA LEU SER GLY PHE SER SEQRES 21 A 606 LEU GLN SER CYS ARG HIS SER ILE PRO VAL PHE CYS HIS SEQRES 22 A 606 SER SER PHE TYR HIS ASP THR ASP PHE LEU GLY GLU GLU SEQRES 23 A 606 LEU ASP ILE VAL ALA ALA LYS SER HIS GLU ALA CYS GLN SEQRES 24 A 606 LYS LEU CYS THR ASN ALA VAL ARG CYS GLN PHE PHE THR SEQRES 25 A 606 TYR THR PRO ALA GLN ALA SER CYS ASN GLU GLY LYS GLY SEQRES 26 A 606 LYS CYS TYR LEU LYS LEU SER SER ASN GLY SER PRO THR SEQRES 27 A 606 LYS ILE LEU HIS GLY ARG GLY GLY ILE SER GLY TYR THR SEQRES 28 A 606 LEU ARG LEU CYS LYS MET ASP ASN GLU CYS THR THR LYS SEQRES 29 A 606 ILE LYS PRO ARG ILE VAL GLY GLY THR ALA SER VAL ARG SEQRES 30 A 606 GLY GLU TRP PRO TRP GLN VAL THR LEU HIS THR THR SER SEQRES 31 A 606 PRO THR GLN ARG HIS LEU CYS GLY GLY SER ILE ILE GLY SEQRES 32 A 606 ASN GLN TRP ILE LEU THR ALA ALA HIS CYS PHE TYR GLY SEQRES 33 A 606 VAL GLU SER PRO LYS ILE LEU ARG VAL TYR SER GLY ILE SEQRES 34 A 606 LEU ASN GLN SER GLU ILE LYS GLU ASP THR SER PHE PHE SEQRES 35 A 606 GLY VAL GLN GLU ILE ILE ILE HIS ASP GLN TYR LYS MET SEQRES 36 A 606 ALA GLU SER GLY TYR ASP ILE ALA LEU LEU LYS LEU GLU SEQRES 37 A 606 THR THR VAL ASN TYR THR ASP SER GLN ARG PRO ILE CYS SEQRES 38 A 606 LEU PRO SER LYS GLY ASP ARG ASN VAL ILE TYR THR ASP SEQRES 39 A 606 CYS TRP VAL THR GLY TRP GLY TYR ARG LYS LEU ARG ASP SEQRES 40 A 606 LYS ILE GLN ASN THR LEU GLN LYS ALA LYS ILE PRO LEU SEQRES 41 A 606 VAL THR ASN GLU GLU CYS GLN LYS ARG TYR ARG GLY HIS SEQRES 42 A 606 LYS ILE THR HIS LYS MET ILE CYS ALA GLY TYR ARG GLU SEQRES 43 A 606 GLY GLY LYS ASP ALA CYS LYS GLY ASP SER GLY GLY PRO SEQRES 44 A 606 LEU SER CYS LYS HIS ASN GLU VAL TRP HIS LEU VAL GLY SEQRES 45 A 606 ILE THR SER TRP GLY GLU GLY CYS ALA GLN ARG GLU ARG SEQRES 46 A 606 PRO GLY VAL TYR THR ASN VAL VAL GLU TYR VAL ASP TRP SEQRES 47 A 606 ILE LEU GLU LYS THR GLN ALA VAL SEQRES 1 K 9 HIS ILE TYR PRO ASP PHE PRO THR ASP MODRES 5EOK NAG A 701 NAG -D MODRES 5EOK NAG B 1 NAG -D MODRES 5EOK NAG A 705 NAG -D MODRES 5EOK NAG A 706 NAG -D MODRES 5EOK NAG B 2 NAG -D MODRES 5EOK FUC B 3 FUC -L HET NAG B 1 14 HET NAG B 2 14 HET FUC B 3 10 HET NAG A 701 14 HET NAG A 705 14 HET NAG A 706 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE FORMUL 3 NAG 5(C8 H15 N O6) FORMUL 3 FUC C6 H12 O5 FORMUL 7 HOH *2(H2 O) HELIX 1 AA1 SER A 24 HIS A 35 1 12 HELIX 2 AA2 ASP A 51 TRP A 55 5 5 HELIX 3 AA3 SER A 114 ASP A 125 1 12 HELIX 4 AA4 LEU A 172 CYS A 175 5 4 HELIX 5 AA5 ASP A 204 HIS A 214 1 11 HELIX 6 AA6 LYS A 230 ARG A 234 5 5 HELIX 7 AA7 LEU A 262 ARG A 266 5 5 HELIX 8 AA8 SER A 295 ASN A 305 1 11 HELIX 9 AA9 LEU A 353 ASP A 359 5 7 HELIX 10 AB1 ASN A 360 THR A 364 5 5 HELIX 11 AB2 ALA A 411 TYR A 416 5 6 HELIX 12 AB3 SER A 420 LYS A 422 5 3 HELIX 13 AB4 SER A 485 ARG A 489 5 5 HELIX 14 AB5 THR A 523 TYR A 531 1 9 HELIX 15 AB6 TYR A 596 LYS A 603 1 8 SHEET 1 AA1 5 LEU A 7 PHE A 12 0 SHEET 2 AA1 5 ARG A 70 TYR A 80 -1 O ARG A 73 N ASP A 9 SHEET 3 AA1 5 LEU A 40 THR A 44 -1 N PHE A 43 O ILE A 77 SHEET 4 AA1 5 THR A 57 LYS A 61 -1 O LYS A 61 N LEU A 40 SHEET 5 AA1 5 ASP A 16 PHE A 21 -1 N VAL A 20 O CYS A 58 SHEET 1 AA2 5 ILE A 96 LYS A 103 0 SHEET 2 AA2 5 ARG A 159 PHE A 170 -1 O ARG A 159 N LYS A 103 SHEET 3 AA2 5 PHE A 130 ALA A 134 -1 N TYR A 133 O VAL A 167 SHEET 4 AA2 5 ILE A 146 HIS A 151 -1 O LEU A 148 N THR A 132 SHEET 5 AA2 5 ILE A 105 VAL A 111 -1 N SER A 110 O CYS A 147 SHEET 1 AA3 5 PHE A 187 ALA A 193 0 SHEET 2 AA3 5 THR A 249 PHE A 260 -1 O SER A 258 N PHE A 187 SHEET 3 AA3 5 PHE A 220 PHE A 224 -1 N PHE A 223 O LEU A 257 SHEET 4 AA3 5 LEU A 236 THR A 241 -1 O LEU A 238 N THR A 222 SHEET 5 AA3 5 SER A 195 MET A 201 -1 N VAL A 200 O CYS A 237 SHEET 1 AA4 2 THR A 281 LEU A 284 0 SHEET 2 AA4 2 LYS A 340 HIS A 343 -1 O LYS A 340 N LEU A 284 SHEET 1 AA5 4 GLU A 286 ALA A 293 0 SHEET 2 AA5 4 GLY A 326 LEU A 332 -1 O CYS A 328 N VAL A 291 SHEET 3 AA5 4 PHE A 311 THR A 315 -1 N THR A 313 O TYR A 329 SHEET 4 AA5 4 ILE A 348 TYR A 351 -1 O ILE A 348 N TYR A 314 SHEET 1 AA6 7 GLN A 384 THR A 389 0 SHEET 2 AA6 7 ARG A 395 GLY A 404 -1 O ARG A 395 N THR A 389 SHEET 3 AA6 7 TRP A 407 THR A 410 -1 O LEU A 409 N SER A 401 SHEET 4 AA6 7 ALA A 464 LEU A 468 -1 O ALA A 464 N THR A 410 SHEET 5 AA6 7 PHE A 443 ILE A 450 -1 N ILE A 449 O LEU A 465 SHEET 6 AA6 7 LEU A 424 TYR A 427 -1 N VAL A 426 O PHE A 443 SHEET 7 AA6 7 GLN A 384 THR A 389 -1 N HIS A 388 O ARG A 425 SHEET 1 AA7 7 GLN A 515 ILE A 519 0 SHEET 2 AA7 7 CYS A 496 GLY A 500 -1 N GLY A 500 O GLN A 515 SHEET 3 AA7 7 PRO A 560 HIS A 565 -1 O SER A 562 N TRP A 497 SHEET 4 AA7 7 VAL A 568 THR A 575 -1 O GLY A 573 N LEU A 561 SHEET 5 AA7 7 GLY A 588 ASN A 592 -1 O THR A 591 N ILE A 574 SHEET 6 AA7 7 MET A 540 ALA A 543 -1 N ILE A 541 O TYR A 590 SHEET 7 AA7 7 LEU A 521 VAL A 522 -1 N VAL A 522 O CYS A 542 SSBOND 1 CYS A 2 CYS A 85 1555 1555 2.07 SSBOND 2 CYS A 28 CYS A 58 1555 1555 2.02 SSBOND 3 CYS A 32 CYS A 38 1555 1555 2.10 SSBOND 4 CYS A 92 CYS A 175 1555 1555 2.05 SSBOND 5 CYS A 118 CYS A 147 1555 1555 2.07 SSBOND 6 CYS A 122 CYS A 128 1555 1555 2.09 SSBOND 7 CYS A 182 CYS A 265 1555 1555 2.05 SSBOND 8 CYS A 208 CYS A 237 1555 1555 2.05 SSBOND 9 CYS A 212 CYS A 218 1555 1555 2.12 SSBOND 10 CYS A 273 CYS A 356 1555 1555 2.07 SSBOND 11 CYS A 299 CYS A 328 1555 1555 2.05 SSBOND 12 CYS A 303 CYS A 309 1555 1555 2.13 SSBOND 13 CYS A 321 CYS A 321 1555 7555 2.39 SSBOND 14 CYS A 362 CYS A 482 1555 1555 2.07 SSBOND 15 CYS A 398 CYS A 414 1555 1555 2.07 SSBOND 16 CYS A 496 CYS A 563 1555 1555 2.07 SSBOND 17 CYS A 527 CYS A 542 1555 1555 2.06 LINK ND2 ASN A 72 C1 NAG A 701 1555 1555 1.45 LINK ND2 ASN A 108 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 432 C1 NAG A 705 1555 1555 1.47 LINK ND2 ASN A 473 C1 NAG A 706 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.47 LINK O6 NAG B 1 C1 FUC B 3 1555 1555 1.45 CISPEP 1 LYS A 8 ASP A 9 0 9.28 CISPEP 2 ILE A 370 VAL A 371 0 0.61 CISPEP 3 GLY A 372 GLY A 373 0 4.16 CISPEP 4 GLY A 373 THR A 374 0 18.53 CISPEP 5 SER A 391 PRO A 392 0 8.14 CRYST1 81.330 81.330 252.219 90.00 90.00 90.00 P 43 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 0.012296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003965 0.00000