HEADER HYDROLASE/HYDROLASE INHIBITOR 28-MAR-07 2PBK TITLE CRYSTAL STRUCTURE OF KSHV PROTEASE IN COMPLEX WITH HEXAPEPTIDE TITLE 2 PHOSPHONATE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: KSHV PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEXAPEPTIDE PHOSPHONATE INHIBITOR; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS; SOURCE 3 ORGANISM_TAXID: 37296; SOURCE 4 STRAIN: 8; SOURCE 5 GENE: AF010430; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SOLID PHASE FMOC KEYWDS KSHV, KSHV PROTEASE, HERPESVIRUS PROTEASE, VIRAL PROTEASE, VIRAL KEYWDS 2 PROTEIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.LAZIC,D.H.GOETZ REVDAT 6 15-NOV-23 2PBK 1 LINK REVDAT 5 30-AUG-23 2PBK 1 REMARK REVDAT 4 20-OCT-21 2PBK 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2PBK 1 VERSN REVDAT 2 24-FEB-09 2PBK 1 VERSN REVDAT 1 25-DEC-07 2PBK 0 JRNL AUTH A.LAZIC,D.H.GOETZ,A.M.NOMURA,A.B.MARNETT,C.S.CRAIK JRNL TITL SUBSTRATE MODULATION OF ENZYME ACTIVITY IN THE HERPESVIRUS JRNL TITL 2 PROTEASE FAMILY. JRNL REF J.MOL.BIOL. V. 373 913 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17870089 JRNL DOI 10.1016/J.JMB.2007.07.073 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 47865 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2568 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2311 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3613 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 530 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.020 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3709 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3465 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5069 ; 1.485 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8025 ; 0.816 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 470 ; 5.883 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;31.819 ;23.050 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;12.128 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.332 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 602 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4063 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 718 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 817 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3631 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1804 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2232 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 394 ; 0.193 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.052 ; 0.200 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): 11 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.246 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.158 ; 0.200 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): 2422 ; 1.085 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 933 ; 0.273 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3834 ; 1.639 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1448 ; 2.362 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1230 ; 3.535 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 230 REMARK 3 RESIDUE RANGE : D 1 D 6 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2530 17.8120 23.4230 REMARK 3 T TENSOR REMARK 3 T11: -0.1043 T22: -0.1290 REMARK 3 T33: -0.1214 T12: -0.0058 REMARK 3 T13: 0.0076 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.1594 L22: 1.6779 REMARK 3 L33: 1.7068 L12: 0.4254 REMARK 3 L13: -0.0432 L23: -0.8420 REMARK 3 S TENSOR REMARK 3 S11: 0.0143 S12: -0.0320 S13: 0.0140 REMARK 3 S21: -0.0138 S22: -0.0083 S23: 0.0072 REMARK 3 S31: -0.2453 S32: 0.0508 S33: -0.0060 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 230 REMARK 3 RESIDUE RANGE : C 1 C 6 REMARK 3 ORIGIN FOR THE GROUP (A): -23.2120 -5.1090 43.3780 REMARK 3 T TENSOR REMARK 3 T11: -0.1512 T22: -0.1332 REMARK 3 T33: -0.1223 T12: -0.0003 REMARK 3 T13: -0.0218 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.6182 L22: 1.4778 REMARK 3 L33: 1.3501 L12: -0.1753 REMARK 3 L13: -0.0940 L23: -0.0825 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.0562 S13: -0.0410 REMARK 3 S21: 0.0538 S22: 0.0374 S23: 0.0136 REMARK 3 S31: 0.1014 S32: -0.0802 S33: -0.0543 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2PBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 61.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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 1FL1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M NAFORMATE, 0.1M NAACETATE, 5% PEG REMARK 280 3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 54.47050 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 400 REMARK 400 COMPOUND REMARK 400 THE ELECTRON DENSITY SURROUNDING THE PHOSPHONATE GROUP SHOWS THAT REMARK 400 THE INHIBITOR IN THE CRYSTAL EXISTS IN AN "AGED" FORM, WHERE THE REMARK 400 PHENOXY GROUPS ATTACHED TO O1A AND O1B ARE RELEASED. IN ADDITION TO REMARK 400 THE COVALENT LINK TO THE CATALYTIC SER 114, THE PHOSPHONATE IS REMARK 400 STABILIZED BY A H BOND TO NE2 OF HIS 46 REMARK 400 REMARK 400 THE 1-ACETYL-L-PROLYL-L-VALYL-L-TYROSYL-3-METHYL-L-VALYL-N~1~-[(1R)- REMARK 400 1-PHOSPHONOETHYL]-L-GLUTAMAMIDE IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: 1-ACETYL-L-PROLYL-L-VALYL-L-TYROSYL-3-METHYL-L-VALYL-N~1~- REMARK 400 [(1R)-1-PHOSPHONOETHYL]-L-GLUTAMAMIDE REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 B 126 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 ASP B 28 CB CG OD1 OD2 REMARK 470 LYS B 99 CD CE NZ REMARK 470 GLU B 155 CD OE1 OE2 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 LYS A 18 CG REMARK 480 GLU A 78 CG CD OE1 OE2 REMARK 480 LYS A 99 CD CE NZ REMARK 480 GLN B 29 CG CD OE1 NE2 REMARK 480 ARG B 91 NE CZ NH1 NH2 REMARK 480 LYS B 95 CE NZ REMARK 480 GLN B 125 CB CG CD OE1 NE2 REMARK 480 LYS B 166 CD CE NZ REMARK 480 ARG B 180 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 214 NZ 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 HOH A 633 O HOH A 843 1.88 REMARK 500 O HOH B 843 O HOH B 856 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 842 O HOH B 827 2556 2.10 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 LYS A 18 CG LYS A 18 CD 0.728 REMARK 500 GLU A 78 CB GLU A 78 CG -0.161 REMARK 500 CYS B 16 CB CYS B 16 SG -0.179 REMARK 500 GLU B 22 CD GLU B 22 OE2 0.075 REMARK 500 GLN B 29 CB GLN B 29 CG -0.514 REMARK 500 ARG B 91 CD ARG B 91 NE -0.377 REMARK 500 LYS B 95 CD LYS B 95 CE -0.450 REMARK 500 GLN B 125 CA GLN B 125 CB -0.150 REMARK 500 LYS B 166 CG LYS B 166 CD -0.308 REMARK 500 ARG B 180 CB ARG B 180 CG -0.195 REMARK 500 MET B 197 CB MET B 197 CG 0.204 REMARK 500 LYS B 214 CE LYS B 214 NZ -0.309 REMARK 500 GLN D 6 C GG7 D 7 N 0.172 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 LYS A 18 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 LYS A 18 CB - CG - CD ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG B 91 CG - CD - NE ANGL. DEV. = 14.2 DEGREES REMARK 500 LYS B 95 CG - CD - CE ANGL. DEV. = 23.1 DEGREES REMARK 500 GLN B 125 CB - CA - C ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG B 144 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LYS B 166 CB - CG - CD ANGL. DEV. = 18.2 DEGREES REMARK 500 LYS B 166 CG - CD - CE ANGL. DEV. = 19.2 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 A 96 -1.85 82.23 REMARK 500 GLN A 125 -146.39 -95.42 REMARK 500 LEU A 140 129.18 -170.22 REMARK 500 THR A 146 34.80 -98.19 REMARK 500 SER B 15 41.77 -97.52 REMARK 500 LEU B 19 -58.93 -151.50 REMARK 500 PRO B 93 150.63 -49.73 REMARK 500 LEU B 140 128.03 -171.14 REMARK 500 THR B 146 37.71 -99.94 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 ACT A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF HEXAPEPTIDE REMARK 800 PHOSPHONATE INHIBITOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF HEXAPEPTIDE REMARK 800 PHOSPHONATE INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FL1 RELATED DB: PDB DBREF 2PBK A 3 230 UNP O36607 O36607_HHV8 3 230 DBREF 2PBK B 3 230 UNP O36607 O36607_HHV8 3 230 DBREF 2PBK C 1 7 PDB 2PBK 2PBK 1 7 DBREF 2PBK D 1 7 PDB 2PBK 2PBK 1 7 SEQADV 2PBK GLY A 204 UNP O36607 SER 204 ENGINEERED MUTATION SEQADV 2PBK GLY B 204 UNP O36607 SER 204 ENGINEERED MUTATION SEQRES 1 A 228 GLN GLY LEU TYR VAL GLY GLY PHE VAL ASP VAL VAL SER SEQRES 2 A 228 CYS PRO LYS LEU GLU GLN GLU LEU TYR LEU ASP PRO ASP SEQRES 3 A 228 GLN VAL THR ASP TYR LEU PRO VAL THR GLU PRO LEU PRO SEQRES 4 A 228 ILE THR ILE GLU HIS LEU PRO GLU THR GLU VAL GLY TRP SEQRES 5 A 228 THR LEU GLY LEU PHE GLN VAL SER HIS GLY ILE PHE CYS SEQRES 6 A 228 THR GLY ALA ILE THR SER PRO ALA PHE LEU GLU LEU ALA SEQRES 7 A 228 SER ARG LEU ALA ASP THR SER HIS VAL ALA ARG ALA PRO SEQRES 8 A 228 VAL LYS ASN LEU PRO LYS GLU PRO LEU LEU GLU ILE LEU SEQRES 9 A 228 HIS THR TRP LEU PRO GLY LEU SER LEU SER SER ILE HIS SEQRES 10 A 228 PRO ARG GLU LEU SER GLN THR PRO SER GLY PRO VAL PHE SEQRES 11 A 228 GLN HIS VAL SER LEU CYS ALA LEU GLY ARG ARG ARG GLY SEQRES 12 A 228 THR VAL ALA VAL TYR GLY HIS ASP ALA GLU TRP VAL VAL SEQRES 13 A 228 SER ARG PHE SER SER VAL SER LYS SER GLU ARG ALA HIS SEQRES 14 A 228 ILE LEU GLN HIS VAL SER SER CYS ARG LEU GLU ASP LEU SEQRES 15 A 228 SER THR PRO ASN PHE VAL SER PRO LEU GLU THR LEU MET SEQRES 16 A 228 ALA LYS ALA ILE ASP ALA GLY PHE ILE ARG ASP ARG LEU SEQRES 17 A 228 ASP LEU LEU LYS THR ASP ARG GLY VAL ALA SER ILE LEU SEQRES 18 A 228 SER PRO VAL TYR LEU LYS ALA SEQRES 1 B 228 GLN GLY LEU TYR VAL GLY GLY PHE VAL ASP VAL VAL SER SEQRES 2 B 228 CYS PRO LYS LEU GLU GLN GLU LEU TYR LEU ASP PRO ASP SEQRES 3 B 228 GLN VAL THR ASP TYR LEU PRO VAL THR GLU PRO LEU PRO SEQRES 4 B 228 ILE THR ILE GLU HIS LEU PRO GLU THR GLU VAL GLY TRP SEQRES 5 B 228 THR LEU GLY LEU PHE GLN VAL SER HIS GLY ILE PHE CYS SEQRES 6 B 228 THR GLY ALA ILE THR SER PRO ALA PHE LEU GLU LEU ALA SEQRES 7 B 228 SER ARG LEU ALA ASP THR SER HIS VAL ALA ARG ALA PRO SEQRES 8 B 228 VAL LYS ASN LEU PRO LYS GLU PRO LEU LEU GLU ILE LEU SEQRES 9 B 228 HIS THR TRP LEU PRO GLY LEU SER LEU SER SER ILE HIS SEQRES 10 B 228 PRO ARG GLU LEU SER GLN THR PRO SER GLY PRO VAL PHE SEQRES 11 B 228 GLN HIS VAL SER LEU CYS ALA LEU GLY ARG ARG ARG GLY SEQRES 12 B 228 THR VAL ALA VAL TYR GLY HIS ASP ALA GLU TRP VAL VAL SEQRES 13 B 228 SER ARG PHE SER SER VAL SER LYS SER GLU ARG ALA HIS SEQRES 14 B 228 ILE LEU GLN HIS VAL SER SER CYS ARG LEU GLU ASP LEU SEQRES 15 B 228 SER THR PRO ASN PHE VAL SER PRO LEU GLU THR LEU MET SEQRES 16 B 228 ALA LYS ALA ILE ASP ALA GLY PHE ILE ARG ASP ARG LEU SEQRES 17 B 228 ASP LEU LEU LYS THR ASP ARG GLY VAL ALA SER ILE LEU SEQRES 18 B 228 SER PRO VAL TYR LEU LYS ALA SEQRES 1 C 7 ACE PRO VAL TYR TBG GLN GG7 SEQRES 1 D 7 ACE PRO VAL TYR TBG GLN GG7 MODRES 2PBK TBG C 5 VAL 3-METHYL-L-VALINE MODRES 2PBK TBG D 5 VAL 3-METHYL-L-VALINE HET ACE C 1 2 HET TBG C 5 8 HET GG7 C 7 6 HET ACE D 1 2 HET TBG D 5 8 HET GG7 D 7 6 HET ACT A 601 4 HET ACT A 602 4 HET ACT B 603 4 HETNAM ACE ACETYL GROUP HETNAM TBG 3-METHYL-L-VALINE HETNAM GG7 [(1R)-1-AMINOETHYL]PHOSPHONIC ACID HETNAM ACT ACETATE ION FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 TBG 2(C6 H13 N O2) FORMUL 3 GG7 2(C2 H8 N O3 P) FORMUL 5 ACT 3(C2 H3 O2 1-) FORMUL 8 HOH *530(H2 O) HELIX 1 1 GLU A 20 TYR A 24 5 5 HELIX 2 2 ASP A 26 THR A 31 1 6 HELIX 3 3 ASP A 32 LEU A 34 5 3 HELIX 4 4 SER A 73 SER A 87 1 15 HELIX 5 5 GLU A 100 LEU A 110 1 11 HELIX 6 6 HIS A 119 SER A 124 1 6 HELIX 7 7 ASP A 153 ARG A 160 1 8 HELIX 8 8 SER A 165 CYS A 179 1 15 HELIX 9 9 ARG A 180 LEU A 184 5 5 HELIX 10 10 PRO A 192 GLY A 204 1 13 HELIX 11 11 ASP A 208 ALA A 220 1 13 HELIX 12 12 GLU B 20 TYR B 24 5 5 HELIX 13 13 ASP B 26 THR B 31 1 6 HELIX 14 14 ASP B 32 LEU B 34 5 3 HELIX 15 15 SER B 73 SER B 87 1 15 HELIX 16 16 SER B 87 ALA B 92 1 6 HELIX 17 17 GLU B 100 LEU B 110 1 11 HELIX 18 18 PRO B 120 LEU B 123 5 4 HELIX 19 19 ASP B 153 ARG B 160 1 8 HELIX 20 20 SER B 165 SER B 178 1 14 HELIX 21 21 CYS B 179 LEU B 184 5 6 HELIX 22 22 PRO B 192 PHE B 205 1 14 HELIX 23 23 ASP B 208 ALA B 220 1 13 SHEET 1 A 8 VAL A 149 GLY A 151 0 SHEET 2 A 8 TYR A 6 VAL A 13 -1 N TYR A 6 O GLY A 151 SHEET 3 A 8 GLY A 64 ILE A 71 -1 O CYS A 67 N GLY A 9 SHEET 4 A 8 GLY A 53 VAL A 61 -1 N LEU A 56 O THR A 68 SHEET 5 A 8 PRO A 41 ILE A 44 -1 N ILE A 42 O GLY A 53 SHEET 6 A 8 PHE A 132 CYS A 138 1 O LEU A 137 N THR A 43 SHEET 7 A 8 GLY A 112 ILE A 118 -1 N GLY A 112 O CYS A 138 SHEET 8 A 8 TYR D 4 TBG D 5 -1 O TBG D 5 N SER A 117 SHEET 1 B 8 VAL B 149 GLY B 151 0 SHEET 2 B 8 TYR B 6 VAL B 13 -1 N TYR B 6 O GLY B 151 SHEET 3 B 8 GLY B 64 ILE B 71 -1 O CYS B 67 N GLY B 9 SHEET 4 B 8 GLY B 53 VAL B 61 -1 N PHE B 59 O PHE B 66 SHEET 5 B 8 PRO B 41 ILE B 44 -1 N ILE B 42 O GLY B 53 SHEET 6 B 8 PHE B 132 CYS B 138 1 O LEU B 137 N THR B 43 SHEET 7 B 8 GLY B 112 ILE B 118 -1 N GLY B 112 O CYS B 138 SHEET 8 B 8 TYR C 4 TBG C 5 -1 O TBG C 5 N SER B 117 LINK OG SER A 114 P GG7 D 7 1555 1555 1.63 LINK OG SER B 114 P GG7 C 7 1555 1555 1.59 LINK C ACE C 1 N PRO C 2 1555 1555 1.31 LINK C TYR C 4 N TBG C 5 1555 1555 1.33 LINK C TBG C 5 N GLN C 6 1555 1555 1.33 LINK C GLN C 6 N GG7 C 7 1555 1555 1.36 LINK C ACE D 1 N PRO D 2 1555 1555 1.34 LINK C TYR D 4 N TBG D 5 1555 1555 1.33 LINK C TBG D 5 N GLN D 6 1555 1555 1.32 LINK C GLN D 6 N GG7 D 7 1555 1555 1.51 CISPEP 1 LEU A 34 PRO A 35 0 2.78 CISPEP 2 SER A 224 PRO A 225 0 0.42 CISPEP 3 LEU B 34 PRO B 35 0 -0.52 CISPEP 4 SER B 224 PRO B 225 0 -7.39 SITE 1 AC1 8 ASP A 12 VAL A 14 LEU A 25 PRO A 27 SITE 2 AC1 8 GLN A 60 GLY A 64 ILE A 65 HOH A 643 SITE 1 AC2 5 GLU A 100 PRO A 101 LEU A 102 LEU A 103 SITE 2 AC2 5 HIS A 152 SITE 1 AC3 4 PRO B 39 SER B 185 HOH B 813 HOH B 819 SITE 1 AC4 27 GLU B 22 HIS B 46 SER B 114 LEU B 115 SITE 2 AC4 27 SER B 116 SER B 117 ILE B 118 HIS B 119 SITE 3 AC4 27 ARG B 121 GLU B 122 SER B 128 GLY B 129 SITE 4 AC4 27 PRO B 130 GLN B 133 GLY B 141 ARG B 142 SITE 5 AC4 27 ARG B 143 HOH B 654 HOH C 8 HOH C 9 SITE 6 AC4 27 HOH C 10 HOH C 11 HOH C 12 HOH C 13 SITE 7 AC4 27 HOH C 14 HOH C 15 HOH C 17 SITE 1 AC5 21 GLU A 22 HIS A 46 SER A 114 LEU A 115 SITE 2 AC5 21 SER A 116 SER A 117 ILE A 118 HIS A 119 SITE 3 AC5 21 GLU A 122 PRO A 130 GLY A 141 ARG A 142 SITE 4 AC5 21 ARG A 143 HOH A 606 HOH A 754 HOH D 8 SITE 5 AC5 21 HOH D 9 HOH D 10 HOH D 11 HOH D 12 SITE 6 AC5 21 HOH D 13 CRYST1 45.883 108.941 54.051 90.00 103.71 90.00 P 1 21 1 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 0.021795 0.000000 0.005317 0.00000 SCALE2 0.000000 0.009179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019044 0.00000