HEADER HYDROLASE 13-OCT-19 6T49 TITLE 3C-LIKE PROTEASE FROM SOUTHAMPTON VIRUS COMPLEXED WITH FMOPL000582A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.15,3.4.22.66,2.7.7.48; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GENOME POLYPROTEIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.6.1.15,3.4.22.66,2.7.7.48; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOUTHAMPTON VIRUS (SEROTYPE 3); SOURCE 3 ORGANISM_TAXID: 37129; SOURCE 4 GENE: ORF1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SOUTHAMPTON VIRUS (SEROTYPE 3); SOURCE 9 ORGANISM_TAXID: 37129; SOURCE 10 GENE: ORF1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS VIRAL PROTEASE., HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GUO,J.B.COOPER REVDAT 2 24-JAN-24 6T49 1 REMARK REVDAT 1 19-AUG-20 6T49 0 JRNL AUTH J.GUO,A.DOUANGAMATH,W.SONG,A.R.COKER,A.W.E.CHAN,S.P.WOOD, JRNL AUTH 2 J.B.COOPER,E.RESNICK,N.LONDON,F.V.DELFT JRNL TITL IN CRYSTALLO-SCREENING FOR DISCOVERY OF HUMAN NOROVIRUS JRNL TITL 2 3C-LIKE PROTEASE INHIBITORS. JRNL REF J STRUCT BIOL X V. 4 00031 2020 JRNL REFN ESSN 2590-1524 JRNL PMID 32743543 JRNL DOI 10.1016/J.YJSBX.2020.100031 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 44479 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2222 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3177 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2701 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2576 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3673 ; 1.837 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5948 ; 1.397 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 352 ; 8.240 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;26.304 ;20.092 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;14.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.778 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 359 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3041 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 589 ; 0.002 ; 0.020 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): 5277 ; 3.359 ; 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 : NULL 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 ANISOTROPIC U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6T49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47120 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 60.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6T1Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT CONCENTRATION OF 5 MG/ML OR REMARK 280 10 MG/ML WITH 0.2 M AMMONIUM CITRATE AND 12% (V/V) PEG3350., PH REMARK 280 5.1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.35200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.65150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.35200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.65150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 391 LIES ON A SPECIAL POSITION. 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 OXT GLN A 172 O HOH A 301 2.00 REMARK 500 O HOH A 409 O HOH A 412 2.19 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 378 O HOH B 469 2558 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 A 59 CG - CD - NE ANGL. DEV. = -15.7 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 ASP A 90 103.53 -50.23 REMARK 500 SER A 91 50.84 117.64 REMARK 500 ALA A 148 -107.58 -7.92 REMARK 500 GLN B 110 57.39 37.71 REMARK 500 ALA B 125 -69.97 -4.04 REMARK 500 ALA B 127 -52.79 -136.04 REMARK 500 LYS B 128 38.80 27.64 REMARK 500 ALA B 148 -126.04 53.73 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 ASP A 90 SER A 91 148.39 REMARK 500 ARG A 147 ALA A 148 146.31 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 A 408 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 409 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 410 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 411 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A 412 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH A 413 DISTANCE = 8.22 ANGSTROMS REMARK 525 HOH A 414 DISTANCE = 8.55 ANGSTROMS REMARK 525 HOH A 415 DISTANCE = 8.85 ANGSTROMS REMARK 525 HOH B 494 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B 495 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH B 496 DISTANCE = 7.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MH5 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IPH RELATED DB: PDB REMARK 900 COMPLEX WITH POLYPEPTIDE INHIBITOR. REMARK 900 RELATED ID: 6T1Q RELATED DB: PDB REMARK 900 NATIVE STRUCTURE. DBREF 6T49 A 1 172 UNP Q04544 POLG_SOUV3 1100 1271 DBREF 6T49 B 4 173 UNP Q04544 POLG_SOUV3 1103 1272 SEQRES 1 A 172 ALA PRO PRO THR LEU TRP SER ARG VAL THR LYS PHE GLY SEQRES 2 A 172 SER GLY TRP GLY PHE TRP VAL SER PRO THR VAL PHE ILE SEQRES 3 A 172 THR THR THR HIS VAL ILE PRO THR SER ALA LYS GLU PHE SEQRES 4 A 172 PHE GLY GLU PRO LEU THR SER ILE ALA ILE HIS ARG ALA SEQRES 5 A 172 GLY GLU PHE THR LEU PHE ARG PHE SER LYS LYS ILE ARG SEQRES 6 A 172 PRO ASP LEU THR GLY MET ILE LEU GLU GLU GLY CYS PRO SEQRES 7 A 172 GLU GLY THR VAL CYS SER VAL LEU ILE LYS ARG ASP SER SEQRES 8 A 172 GLY GLU LEU LEU PRO LEU ALA VAL ARG MET GLY ALA ILE SEQRES 9 A 172 ALA SER MET ARG ILE GLN GLY ARG LEU VAL HIS GLY GLN SEQRES 10 A 172 SER GLY MET LEU LEU THR GLY ALA ASN ALA LYS GLY MET SEQRES 11 A 172 ASP LEU GLY THR ILE PRO GLY ASP CYS GLY ALA PRO TYR SEQRES 12 A 172 VAL TYR LYS ARG ALA ASN ASP TRP VAL VAL CYS GLY VAL SEQRES 13 A 172 HIS ALA ALA ALA THR LYS SER GLY ASN THR VAL VAL CYS SEQRES 14 A 172 ALA VAL GLN SEQRES 1 B 170 THR LEU TRP SER ARG VAL THR LYS PHE GLY SER GLY TRP SEQRES 2 B 170 GLY PHE TRP VAL SER PRO THR VAL PHE ILE THR THR THR SEQRES 3 B 170 HIS VAL ILE PRO THR SER ALA LYS GLU PHE PHE GLY GLU SEQRES 4 B 170 PRO LEU THR SER ILE ALA ILE HIS ARG ALA GLY GLU PHE SEQRES 5 B 170 THR LEU PHE ARG PHE SER LYS LYS ILE ARG PRO ASP LEU SEQRES 6 B 170 THR GLY MET ILE LEU GLU GLU GLY CYS PRO GLU GLY THR SEQRES 7 B 170 VAL CYS SER VAL LEU ILE LYS ARG ASP SER GLY GLU LEU SEQRES 8 B 170 LEU PRO LEU ALA VAL ARG MET GLY ALA ILE ALA SER MET SEQRES 9 B 170 ARG ILE GLN GLY ARG LEU VAL HIS GLY GLN SER GLY MET SEQRES 10 B 170 LEU LEU THR GLY ALA ASN ALA LYS GLY MET ASP LEU GLY SEQRES 11 B 170 THR ILE PRO GLY ASP CYS GLY ALA PRO TYR VAL TYR LYS SEQRES 12 B 170 ARG ALA ASN ASP TRP VAL VAL CYS GLY VAL HIS ALA ALA SEQRES 13 B 170 ALA THR LYS SER GLY ASN THR VAL VAL CYS ALA VAL GLN SEQRES 14 B 170 ALA HET MH5 A 201 17 HET DMS A 202 4 HET DMS A 203 4 HET DMS A 204 4 HET DMS B 301 4 HET PO4 B 302 5 HETNAM MH5 3-[(5-METHYLTHIOPHEN-2-YL)METHYLAMINO]BENZOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM PO4 PHOSPHATE ION FORMUL 3 MH5 C13 H13 N O2 S FORMUL 4 DMS 4(C2 H6 O S) FORMUL 8 PO4 O4 P 3- FORMUL 9 HOH *211(H2 O) HELIX 1 AA1 PRO A 2 SER A 7 1 6 HELIX 2 AA2 HIS A 30 ILE A 32 5 3 HELIX 3 AA3 ILE A 135 CYS A 139 5 5 HELIX 4 AA4 THR B 4 SER B 7 5 4 HELIX 5 AA5 HIS B 30 ILE B 32 5 3 HELIX 6 AA6 THR B 45 ILE B 47 5 3 HELIX 7 AA7 GLY B 129 GLY B 133 5 5 HELIX 8 AA8 ILE B 135 CYS B 139 5 5 SHEET 1 AA1 5 VAL A 9 PHE A 12 0 SHEET 2 AA1 5 GLY A 15 TRP A 19 -1 O GLY A 15 N PHE A 12 SHEET 3 AA1 5 VAL A 24 THR A 28 -1 O ILE A 26 N PHE A 18 SHEET 4 AA1 5 PHE A 55 PHE A 60 -1 O PHE A 58 N PHE A 25 SHEET 5 AA1 5 ILE A 47 ALA A 52 -1 N ALA A 48 O ARG A 59 SHEET 1 AA2 2 GLU A 38 PHE A 39 0 SHEET 2 AA2 2 GLU A 42 PRO A 43 -1 O GLU A 42 N PHE A 39 SHEET 1 AA3 8 ILE A 72 LEU A 73 0 SHEET 2 AA3 8 TRP A 151 ALA A 160 1 O VAL A 153 N ILE A 72 SHEET 3 AA3 8 THR A 166 ALA A 170 -1 O ALA A 170 N VAL A 156 SHEET 4 AA3 8 ARG A 112 LEU A 121 -1 N GLN A 117 O CYS A 169 SHEET 5 AA3 8 GLU A 93 ILE A 109 -1 N ALA A 105 O GLY A 116 SHEET 6 AA3 8 VAL A 82 ARG A 89 -1 N ILE A 87 O LEU A 95 SHEET 7 AA3 8 PRO A 142 LYS A 146 -1 O VAL A 144 N SER A 84 SHEET 8 AA3 8 TRP A 151 ALA A 160 -1 O VAL A 152 N TYR A 145 SHEET 1 AA4 5 VAL B 9 PHE B 12 0 SHEET 2 AA4 5 GLY B 15 TRP B 19 -1 O GLY B 15 N PHE B 12 SHEET 3 AA4 5 VAL B 24 THR B 28 -1 O ILE B 26 N PHE B 18 SHEET 4 AA4 5 PHE B 55 ARG B 59 -1 O PHE B 58 N PHE B 25 SHEET 5 AA4 5 ALA B 48 ALA B 52 -1 N ALA B 52 O PHE B 55 SHEET 1 AA5 2 GLU B 38 PHE B 39 0 SHEET 2 AA5 2 GLU B 42 PRO B 43 -1 O GLU B 42 N PHE B 39 SHEET 1 AA6 8 ILE B 72 LEU B 73 0 SHEET 2 AA6 8 ASP B 150 ALA B 160 1 O VAL B 153 N ILE B 72 SHEET 3 AA6 8 THR B 166 ALA B 170 -1 O ALA B 170 N VAL B 156 SHEET 4 AA6 8 ARG B 112 LEU B 121 -1 N GLN B 117 O CYS B 169 SHEET 5 AA6 8 LEU B 94 ILE B 109 -1 N ILE B 109 O ARG B 112 SHEET 6 AA6 8 VAL B 82 LYS B 88 -1 N ILE B 87 O LEU B 95 SHEET 7 AA6 8 PRO B 142 ARG B 147 -1 O VAL B 144 N SER B 84 SHEET 8 AA6 8 ASP B 150 ALA B 160 -1 O ASP B 150 N ARG B 147 SITE 1 AC1 8 GLN A 110 ARG A 112 THR A 134 ILE A 135 SITE 2 AC1 8 CYS A 139 ALA A 159 ALA A 160 HOH A 318 SITE 1 AC2 5 ARG A 89 MET A 130 ASP A 131 HOH A 366 SITE 2 AC2 5 THR B 4 SITE 1 AC3 8 LEU A 121 ALA A 127 THR A 134 ALA A 160 SITE 2 AC3 8 THR A 161 GLY A 164 ASN A 165 THR A 166 SITE 1 AC4 4 GLU A 75 GLY A 76 CYS A 77 PRO A 78 SITE 1 AC5 3 THR B 10 TRP B 19 ARG B 65 SITE 1 AC6 3 CYS B 77 ILE B 104 GLN B 117 CRYST1 62.704 89.303 60.701 90.00 96.52 90.00 C 1 2 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 0.015948 0.000000 0.001823 0.00000 SCALE2 0.000000 0.011198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016581 0.00000