HEADER BLOOD CLOTTING 17-JAN-25 9I24 TITLE COAGULATION FACTOR XA COMPLEX WITH A2-LOOP PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIVATED FACTOR XA HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FACTOR X LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: COAGULATION FACTOR V HEAVY CHAIN; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: THE Y IS PHOSPHORYLATED (PTR); THE N-TERMINUS IS COMPND 14 ACETYLATED; THE C-TERMINUS IS AMIDATED.; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: GLU-GLY-ARG-CHLOROMETHYL KETONE INHIBITOR (EGRCK); COMPND 17 CHAIN: I; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: THE R IS MODIFIED AND THE IDENTIFIER OGJ IS USED. IT COMPND 20 IS COVALENTLY LINKED TO THE CATALYTIC SER195 AND HIS57. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F10; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEASE, ENZYME, COMPLEX, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HUNTINGTON,F.I.USTOK REVDAT 3 18-FEB-26 9I24 1 JRNL REVDAT 2 11-FEB-26 9I24 1 COMPND REMARK DBREF SHEET REVDAT 2 2 1 LINK ATOM REVDAT 1 26-NOV-25 9I24 0 JRNL AUTH F.I.USTOK,A.FAILLE,J.A.HUNTINGTON JRNL TITL A 3.3- ANGSTROM CRYO-EM STRUCTURE OF AN ENGINEERED JRNL TITL 2 HIGH-AFFINITY HUMAN PROTHROMBINASE COMPLEX. JRNL REF BLOOD V. 147 573 2026 JRNL REFN ESSN 1528-0020 JRNL PMID 41144779 JRNL DOI 10.1182/BLOOD.2025031527 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 89240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.083 REMARK 3 FREE R VALUE TEST SET COUNT : 4536 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6107 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 317 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2262 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.83400 REMARK 3 B22 (A**2) : 0.85100 REMARK 3 B33 (A**2) : -0.01700 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): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.470 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2519 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2257 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3430 ; 1.977 ; 1.827 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5198 ; 0.731 ; 1.761 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 6.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ;12.079 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;11.676 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 368 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3125 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 617 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 522 ; 0.319 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 41 ; 0.211 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1196 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 215 ; 0.288 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.121 ; 0.200 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): 1284 ; 5.816 ; 1.804 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1283 ; 5.815 ; 1.804 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1627 ; 8.127 ; 3.239 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1628 ; 8.125 ; 3.239 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1235 ; 7.564 ; 2.076 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1236 ; 7.561 ; 2.077 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1801 ;10.601 ; 3.694 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1802 ;10.598 ; 3.695 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): 4776 ; 4.060 ; 3.000 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9I24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292144425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-24 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.70979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89301 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 54.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 37.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: IMIDAZOLE, MPD, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.23650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.16750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.20950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.16750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.23650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.20950 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, C, I 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 LYS H 245 REMARK 465 THR H 246 REMARK 465 ARG H 247 REMARK 465 GLY H 248 REMARK 465 LEU H 249 REMARK 465 PRO H 250 REMARK 465 LYS H 251 REMARK 465 ALA H 252 REMARK 465 LYS H 253 REMARK 465 SER H 254 REMARK 465 HIS H 255 REMARK 465 ALA H 256 REMARK 465 PRO H 257 REMARK 465 GLU H 258 REMARK 465 VAL H 259 REMARK 465 ILE H 260 REMARK 465 THR H 261 REMARK 465 SER H 262 REMARK 465 SER H 263 REMARK 465 PRO H 264 REMARK 465 MET L 85 REMARK 465 GLU L 138 REMARK 465 ARG L 139 REMARK 465 CYS C 1 REMARK 465 ILE C 2 REMARK 465 PRO C 3 REMARK 465 ASP C 4 REMARK 465 ASP C 5 REMARK 465 PRO C 21 REMARK 465 ARG I 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS H 23 CD CE NZ REMARK 470 LYS H 62 CG CD CE NZ REMARK 470 GLN H 75 CD OE1 NE2 REMARK 470 GLU H 76 CG CD OE1 OE2 REMARK 470 LYS H 96 CD CE NZ REMARK 470 GLU H 97 CG CD OE1 OE2 REMARK 470 LYS H 134 CG CD CE NZ REMARK 470 LYS H 148 CD CE NZ REMARK 470 ARG H 154 NE CZ NH1 NH2 REMARK 470 LYS H 223 CE NZ REMARK 470 LYS H 230 NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 LYS H 243 CG CD CE NZ REMARK 470 ARG L 86 CG CD NE CZ NH1 NH2 REMARK 470 LYS L 87 CE NZ REMARK 470 GLN L 104 CG CD OE1 NE2 REMARK 470 SER L 106 OG REMARK 470 ARG L 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS L 122 CE NZ REMARK 470 LEU L 137 CG CD1 CD2 REMARK 470 ASP C 6 CG OD1 OD2 REMARK 470 GLU C 7 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 SG CYS H 22 SG CYS H 27 1.68 REMARK 500 NH2 ARG H 107 O HOH H 401 2.07 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 H 63 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET H 131B CG - SD - CE ANGL. DEV. = -19.8 DEGREES REMARK 500 ARG H 165 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 CYS H 182 CA - CB - SG ANGL. DEV. = 6.9 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 ASN H 72 103.34 -160.18 REMARK 500 ARG H 115 -177.00 -171.37 REMARK 500 SER H 214 -61.85 -123.58 REMARK 500 GLN L 98 -102.11 -127.67 REMARK 500 LYS L 122 -56.81 -121.73 REMARK 500 LYS L 122 -47.77 -130.51 REMARK 500 ASP C 8 46.57 -149.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG H 63 0.08 SIDE CHAIN REMARK 500 TYR H 99 0.07 SIDE CHAIN REMARK 500 ARG H 150 0.12 SIDE CHAIN REMARK 500 ARG H 165 0.10 SIDE CHAIN 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 SER C 9 11.46 REMARK 500 PTR C 16 -10.58 REMARK 500 REMARK 500 REMARK: NULL 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 CA H 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP H 70 OD1 REMARK 620 2 ASN H 72 O 84.4 REMARK 620 3 GLN H 75 O 164.3 80.5 REMARK 620 4 GLU H 80 OE2 102.8 170.3 92.7 REMARK 620 5 HOH H 416 O 74.2 100.7 112.7 75.5 REMARK 620 6 HOH H 485 O 82.5 89.8 93.1 97.5 153.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR H 185 O REMARK 620 2 ASP H 185A O 84.2 REMARK 620 3 ARG H 222 O 167.7 90.1 REMARK 620 4 LYS H 224 O 88.2 120.5 85.2 REMARK 620 5 HOH H 450 O 89.4 173.5 96.4 60.1 REMARK 620 6 HOH H 489 O 100.0 88.3 90.7 150.8 91.7 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0GJ H 305 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: GLU GLY AR7 0QE REMARK 630 DETAILS: NULL DBREF 9I24 H 16 264 UNP P00742 FA10_HUMAN 235 486 DBREF 9I24 L 86 139 UNP P00742 FA10_HUMAN 126 179 DBREF 9I24 C 1 21 PDB 9I24 9I24 1 21 DBREF 9I24 I 1 3 PDB 9I24 9I24 1 3 SEQADV 9I24 LYS H 243 UNP P00742 INSERTION SEQADV 9I24 THR H 244 UNP P00742 INSERTION SEQADV 9I24 MET L 85 UNP P00742 INITIATING METHIONINE SEQRES 1 H 254 ILE VAL GLY GLY GLN GLU CYS LYS ASP GLY GLU CYS PRO SEQRES 2 H 254 TRP GLN ALA LEU LEU ILE ASN GLU GLU ASN GLU GLY PHE SEQRES 3 H 254 CYS GLY GLY THR ILE LEU SER GLU PHE TYR ILE LEU THR SEQRES 4 H 254 ALA ALA HIS CYS LEU TYR GLN ALA LYS ARG PHE LYS VAL SEQRES 5 H 254 ARG VAL GLY ASP ARG ASN THR GLU GLN GLU GLU GLY GLY SEQRES 6 H 254 GLU ALA VAL HIS GLU VAL GLU VAL VAL ILE LYS HIS ASN SEQRES 7 H 254 ARG PHE THR LYS GLU THR TYR ASP PHE ASP ILE ALA VAL SEQRES 8 H 254 LEU ARG LEU LYS THR PRO ILE THR PHE ARG MET ASN VAL SEQRES 9 H 254 ALA PRO ALA CYS LEU PRO GLU ARG ASP TRP ALA GLU SER SEQRES 10 H 254 THR LEU MET THR GLN LYS THR GLY ILE VAL SER GLY PHE SEQRES 11 H 254 GLY ARG THR HIS GLU LYS GLY ARG GLN SER THR ARG LEU SEQRES 12 H 254 LYS MET LEU GLU VAL PRO TYR VAL ASP ARG ASN SER CYS SEQRES 13 H 254 LYS LEU SER SER SER PHE ILE ILE THR GLN ASN MET PHE SEQRES 14 H 254 CYS ALA GLY TYR ASP THR LYS GLN GLU ASP ALA CYS GLN SEQRES 15 H 254 GLY ASP SER GLY GLY PRO HIS VAL THR ARG PHE LYS ASP SEQRES 16 H 254 THR TYR PHE VAL THR GLY ILE VAL SER TRP GLY GLU GLY SEQRES 17 H 254 CYS ALA ARG LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 H 254 THR ALA PHE LEU LYS TRP ILE ASP ARG SER MET LYS THR SEQRES 19 H 254 LYS THR ARG GLY LEU PRO LYS ALA LYS SER HIS ALA PRO SEQRES 20 H 254 GLU VAL ILE THR SER SER PRO SEQRES 1 L 55 MET ARG LYS LEU CYS SER LEU ASP ASN GLY ASP CYS ASP SEQRES 2 L 55 GLN PHE CYS HIS GLU GLU GLN ASN SER VAL VAL CYS SER SEQRES 3 L 55 CYS ALA ARG GLY TYR THR LEU ALA ASP ASN GLY LYS ALA SEQRES 4 L 55 CYS ILE PRO THR GLY PRO TYR PRO CYS GLY LYS GLN THR SEQRES 5 L 55 LEU GLU ARG SEQRES 1 C 15 CYS ILE PRO ASP ASP ASP GLU ASP SER PTR GLU ILE PHE SEQRES 2 C 15 GLU PRO SEQRES 1 I 3 GLU GLY ARG MODRES 9I24 PTR C 16 TYR MODIFIED RESIDUE HET PTR C 16 16 HET CA H 301 1 HET NA H 302 1 HET CL H 303 1 HET IMD H 304 5 HET 0GJ H 305 12 HETNAM PTR O-PHOSPHOTYROSINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM IMD IMIDAZOLE HETNAM 0GJ L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO) HETNAM 2 0GJ METHYL]AMINO}-1-[(1S)-2-CHLORO-1- HETNAM 3 0GJ HYDROXYETHYL]BUTYL}GLYCINAMIDE HETSYN PTR PHOSPHONOTYROSINE FORMUL 3 PTR C9 H12 N O6 P FORMUL 5 CA CA 2+ FORMUL 6 NA NA 1+ FORMUL 7 CL CL 1- FORMUL 8 IMD C3 H5 N2 1+ FORMUL 9 0GJ C14 H28 CL N6 O5 1+ FORMUL 10 HOH *295(H2 O) HELIX 1 AA1 ALA H 55 GLN H 61 5 7 HELIX 2 AA2 GLU H 124A THR H 131 1 8 HELIX 3 AA3 ASP H 164 SER H 172 1 9 HELIX 4 AA4 PHE H 234 MET H 242 1 9 HELIX 5 AA5 LEU L 91 CYS L 96 5 6 SHEET 1 AA1 8 GLN H 20 GLU H 21 0 SHEET 2 AA1 8 LYS H 156 VAL H 163 -1 O MET H 157 N GLN H 20 SHEET 3 AA1 8 MET H 180 ALA H 183 -1 O CYS H 182 N VAL H 163 SHEET 4 AA1 8 GLY H 226 LYS H 230 -1 O TYR H 228 N PHE H 181 SHEET 5 AA1 8 THR H 206 TRP H 215 -1 N TRP H 215 O ILE H 227 SHEET 6 AA1 8 PRO H 198 PHE H 203 -1 N HIS H 199 O THR H 210 SHEET 7 AA1 8 THR H 135 GLY H 140 -1 N ILE H 137 O VAL H 200 SHEET 8 AA1 8 LYS H 156 VAL H 163 -1 O VAL H 160 N GLY H 136 SHEET 1 AA2 8 ALA H 81 HIS H 83 0 SHEET 2 AA2 8 LYS H 65 VAL H 68 -1 N VAL H 66 O HIS H 83 SHEET 3 AA2 8 GLN H 30 ILE H 34 -1 N LEU H 32 O ARG H 67 SHEET 4 AA2 8 GLY H 40 ILE H 46 -1 O CYS H 42 N LEU H 33 SHEET 5 AA2 8 TYR H 51 THR H 54 -1 O LEU H 53 N THR H 45 SHEET 6 AA2 8 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 AA2 8 VAL H 85 HIS H 91 -1 N ILE H 89 O VAL H 105 SHEET 8 AA2 8 PTR C 16 PHE C 19 -1 O GLU C 17 N LYS H 90 SHEET 1 AA3 2 PHE L 99 GLU L 103 0 SHEET 2 AA3 2 SER L 106 SER L 110 -1 O VAL L 108 N HIS L 101 SHEET 1 AA4 2 TYR L 115 LEU L 117 0 SHEET 2 AA4 2 CYS L 124 PRO L 126 -1 O ILE L 125 N THR L 116 SSBOND 1 CYS H 22 CYS H 27 1555 1555 2.11 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.07 SSBOND 3 CYS H 122 CYS L 132 1555 1555 2.06 SSBOND 4 CYS H 168 CYS H 182 1555 1555 2.11 SSBOND 5 CYS H 191 CYS H 220 1555 1555 2.07 SSBOND 6 CYS L 89 CYS L 100 1555 1555 2.03 SSBOND 7 CYS L 96 CYS L 109 1555 1555 2.05 SSBOND 8 CYS L 111 CYS L 124 1555 1555 2.08 LINK NE2 HIS H 57 C3 0GJ H 305 1555 1555 1.53 LINK OG SER H 195 C2 0GJ H 305 1555 1555 1.47 LINK N2 0GJ H 305 C GLY I 2 1555 1555 1.36 LINK C SER C 9 N PTR C 16 1555 1555 1.34 LINK C PTR C 16 N GLU C 17 1555 1555 1.32 LINK OD1 ASP H 70 CA CA H 301 1555 1555 2.31 LINK O ASN H 72 CA CA H 301 1555 1555 2.30 LINK O GLN H 75 CA CA H 301 1555 1555 2.21 LINK OE2 GLU H 80 CA CA H 301 1555 1555 2.34 LINK O TYR H 185 NA NA H 302 1555 1555 2.31 LINK O ASP H 185A NA NA H 302 1555 1555 2.43 LINK O ARG H 222 NA NA H 302 1555 1555 2.42 LINK O LYS H 224 NA NA H 302 1555 1555 2.35 LINK CA CA H 301 O HOH H 416 1555 1555 2.65 LINK CA CA H 301 O HOH H 485 1555 1555 2.44 LINK NA NA H 302 O HOH H 450 1555 1555 2.97 LINK NA NA H 302 O HOH H 489 1555 1555 2.30 CRYST1 48.473 72.419 82.335 90.00 90.00 90.00 P 21 21 21 4 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 0.020630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012146 0.00000 CONECT 61 95 CONECT 95 61 CONECT 218 336 CONECT 330 2463 CONECT 336 218 CONECT 442 2444 CONECT 458 2444 CONECT 491 2444 CONECT 532 2444 CONECT 896 2316 CONECT 1316 1433 CONECT 1317 1434 CONECT 1433 1316 CONECT 1434 1317 CONECT 1447 2445 CONECT 1459 2445 CONECT 1516 1740 CONECT 1543 2454 CONECT 1740 1516 CONECT 1750 2445 CONECT 1779 2445 CONECT 1981 2071 CONECT 2037 2147 CONECT 2071 1981 CONECT 2147 2037 CONECT 2159 2250 CONECT 2250 2159 CONECT 2316 896 CONECT 2372 2376 CONECT 2376 2372 2377 CONECT 2377 2376 2378 2380 CONECT 2378 2377 2379 2392 CONECT 2379 2378 CONECT 2380 2377 2381 CONECT 2381 2380 2382 2383 CONECT 2382 2381 2384 CONECT 2383 2381 2385 CONECT 2384 2382 2386 CONECT 2385 2383 2386 CONECT 2386 2384 2385 2387 CONECT 2387 2386 2388 CONECT 2388 2387 2389 2390 2391 CONECT 2389 2388 CONECT 2390 2388 CONECT 2391 2388 CONECT 2392 2378 CONECT 2441 2452 CONECT 2444 442 458 491 532 CONECT 2444 2479 2548 CONECT 2445 1447 1459 1750 1779 CONECT 2445 2513 2552 CONECT 2447 2448 2451 CONECT 2448 2447 2449 CONECT 2449 2448 2450 CONECT 2450 2449 2451 CONECT 2451 2447 2450 CONECT 2452 2441 2453 CONECT 2453 2452 2454 2456 CONECT 2454 1543 2453 2455 2463 CONECT 2455 2454 CONECT 2456 2453 2457 CONECT 2457 2456 2458 CONECT 2458 2457 2459 CONECT 2459 2458 2460 CONECT 2460 2459 2461 2462 CONECT 2461 2460 CONECT 2462 2460 CONECT 2463 330 2454 CONECT 2479 2444 CONECT 2513 2445 CONECT 2548 2444 CONECT 2552 2445 MASTER 429 0 6 5 20 0 0 6 2577 4 72 28 END