HEADER TRANSFERASE/TRANSFERASE INHIBITOR 18-NOV-15 5ETQ TITLE S. AUREUS 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE TITLE 2 COMPLEXED WITH AMPCPP AND INHIBITOR AT 1.96 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ADDITIONAL DENSITY WAS NOTED AT RESIDUE CYS80 IN BOTH COMPND 7 PROTOMERS OF THE ASYMMETRIC UNIT. THIS WAS MODELLED AS THE OXIDIZED COMPND 8 FORM, S-HYDROXY CYSTEINE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: RK60_02090, RK67_01645, RK72_06915, RK74_04210, RK75_00240, SOURCE 5 RK80_01970, RK83_05435, RK84_03130, RK95_04415, RK96_04825, SOURCE 6 RK98_03440, RK99_07885, RL05_10010, RL06_09555, RL08_05305, SOURCE 7 TM59_02255; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, AMPCPP, PYROPHOSPHOKINASE, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.L.DENNIS,T.S.PEAT,J.D.SWARBRICK REVDAT 4 15-NOV-23 5ETQ 1 REMARK REVDAT 3 27-SEP-23 5ETQ 1 JRNL REMARK LINK REVDAT 2 22-JUN-16 5ETQ 1 JRNL REVDAT 1 04-MAY-16 5ETQ 0 JRNL AUTH M.L.DENNIS,N.P.PITCHER,M.D.LEE,A.J.DEBONO,Z.C.WANG, JRNL AUTH 2 J.R.HARJANI,R.RAHMANI,B.CLEARY,T.S.PEAT,J.B.BAELL, JRNL AUTH 3 J.D.SWARBRICK JRNL TITL STRUCTURAL BASIS FOR THE SELECTIVE BINDING OF INHIBITORS TO JRNL TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE FROM JRNL TITL 3 STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI. JRNL REF J.MED.CHEM. V. 59 5248 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27094768 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00002 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22352 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1146 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1619 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2508 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 111 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 2.16000 REMARK 3 B33 (A**2) : -1.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.92000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.179 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2662 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2534 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3628 ; 1.884 ; 2.043 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5836 ; 3.613 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 6.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;35.713 ;24.828 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 468 ;11.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.936 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.252 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2988 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 546 ; 0.009 ; 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): 1254 ; 1.571 ; 0.918 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1253 ; 1.553 ; 0.916 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1564 ; 2.204 ; 1.363 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1565 ; 2.212 ; 1.364 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1408 ; 3.499 ; 1.361 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1409 ; 3.497 ; 1.361 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2065 ; 5.092 ; 1.881 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3066 ; 6.351 ; 8.785 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3067 ; 6.351 ; 8.792 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5ETQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9707 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 68.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 4CWB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 6.9 MG/ML, 1 MM AMPCPP, 1 MM REMARK 280 INHIBITOR, 0.202 M MAGNESIUM CHLORIDE, 0.1 M TRIS CHLORIDE, 20%W/ REMARK 280 V PEG8000, 50 MM SODIUM THIOCYANATE, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 281K 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 34.10000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 LYS A 158 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 LYS B 158 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 ALA A 132 35.23 -146.33 REMARK 500 ALA B 132 35.37 -145.89 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 27 O REMARK 620 2 TYR A 29 O 103.0 REMARK 620 3 ILE A 32 O 89.8 89.4 REMARK 620 4 HOH A 315 O 68.4 169.9 95.6 REMARK 620 5 HOH A 370 O 149.8 106.8 85.4 82.4 REMARK 620 6 HOH B 358 O 100.6 94.8 167.7 82.1 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD2 REMARK 620 2 ASP A 97 OD2 89.8 REMARK 620 3 APC A 203 O3G 176.2 92.5 REMARK 620 4 APC A 203 O2B 99.7 99.3 82.9 REMARK 620 5 HOH A 342 O 87.7 168.3 89.5 92.3 REMARK 620 6 HOH A 355 O 86.2 87.7 90.9 170.8 80.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD1 REMARK 620 2 ASP A 97 OD1 90.4 REMARK 620 3 APC A 203 O2B 93.6 91.9 REMARK 620 4 APC A 203 O2A 95.4 168.6 97.5 REMARK 620 5 HOH A 310 O 89.0 85.1 176.0 85.3 REMARK 620 6 HOH A 327 O 174.8 87.3 91.1 86.1 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 206 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD1 REMARK 620 2 HOH A 333 O 94.4 REMARK 620 3 ASP B 107 OD1 163.8 79.7 REMARK 620 4 HOH B 311 O 80.7 169.4 107.4 REMARK 620 5 HOH B 332 O 84.7 97.6 81.2 91.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 315 O REMARK 620 2 HOH A 370 O 83.4 REMARK 620 3 ASN B 27 O 69.9 96.5 REMARK 620 4 TYR B 29 O 170.1 98.2 100.2 REMARK 620 5 ILE B 32 O 95.0 170.9 91.3 85.0 REMARK 620 6 HOH B 358 O 80.6 81.2 150.4 109.4 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 95 OD1 REMARK 620 2 ASP B 97 OD1 89.8 REMARK 620 3 APC B 203 O2B 90.6 91.9 REMARK 620 4 APC B 203 O1A 89.5 175.3 92.8 REMARK 620 5 HOH B 309 O 89.3 87.5 179.4 87.8 REMARK 620 6 HOH B 341 O 174.9 87.5 93.7 92.9 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 95 OD2 REMARK 620 2 ASP B 97 OD2 86.6 REMARK 620 3 APC B 203 O1G 178.0 95.3 REMARK 620 4 APC B 203 O2B 91.3 97.6 88.0 REMARK 620 5 HOH B 329 O 83.4 165.8 94.8 92.7 REMARK 620 6 HOH B 348 O 87.7 88.5 92.8 173.7 81.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue APC A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YH2 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue APC B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YH2 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4M5H RELATED DB: PDB REMARK 900 4M5H CONTAINS THE SAME INHIBITOR IN THE E. COLI VARIANT OF HPPK REMARK 900 RELATED ID: 5ETK RELATED DB: PDB REMARK 900 RELATED ID: 5ETL RELATED DB: PDB REMARK 900 RELATED ID: 5ETM RELATED DB: PDB REMARK 900 RELATED ID: 5ETN RELATED DB: PDB REMARK 900 RELATED ID: 5ETO RELATED DB: PDB REMARK 900 RELATED ID: 5ETP RELATED DB: PDB REMARK 900 RELATED ID: 5ETR RELATED DB: PDB REMARK 900 RELATED ID: 5ETS RELATED DB: PDB REMARK 900 RELATED ID: 5ETT RELATED DB: PDB REMARK 900 RELATED ID: 5ETV RELATED DB: PDB DBREF1 5ETQ A 1 158 UNP A0A0H1ZSM1_STAAU DBREF2 5ETQ A A0A0H1ZSM1 1 158 DBREF1 5ETQ B 1 158 UNP A0A0H1ZSM1_STAAU DBREF2 5ETQ B A0A0H1ZSM1 1 158 SEQADV 5ETQ GLY A -2 UNP A0A0H1ZSM EXPRESSION TAG SEQADV 5ETQ SER A -1 UNP A0A0H1ZSM EXPRESSION TAG SEQADV 5ETQ HIS A 0 UNP A0A0H1ZSM EXPRESSION TAG SEQADV 5ETQ GLY B -2 UNP A0A0H1ZSM EXPRESSION TAG SEQADV 5ETQ SER B -1 UNP A0A0H1ZSM EXPRESSION TAG SEQADV 5ETQ HIS B 0 UNP A0A0H1ZSM EXPRESSION TAG SEQRES 1 A 161 GLY SER HIS MET ILE GLN ALA TYR LEU GLY LEU GLY SER SEQRES 2 A 161 ASN ILE GLY ASP ARG GLU SER GLN LEU ASN ASP ALA ILE SEQRES 3 A 161 LYS ILE LEU ASN GLU TYR ASP GLY ILE SER VAL SER ASN SEQRES 4 A 161 ILE SER PRO ILE TYR GLU THR ALA PRO VAL GLY TYR THR SEQRES 5 A 161 GLU GLN PRO ASN PHE LEU ASN LEU CYS VAL GLU ILE GLN SEQRES 6 A 161 THR THR LEU THR VAL LEU GLN LEU LEU GLU CYS CYS LEU SEQRES 7 A 161 LYS THR GLU GLU CSO LEU HIS ARG ILE ARG LYS GLU ARG SEQRES 8 A 161 TRP GLY PRO ARG THR LEU ASP VAL ASP ILE LEU LEU TYR SEQRES 9 A 161 GLY GLU GLU MET ILE ASP LEU PRO LYS LEU SER VAL PRO SEQRES 10 A 161 HIS PRO ARG MET ASN GLU ARG ALA PHE VAL LEU ILE PRO SEQRES 11 A 161 LEU ASN ASP ILE ALA ALA ASN VAL VAL GLU PRO ARG SER SEQRES 12 A 161 LYS LEU LYS VAL LYS ASP LEU VAL PHE VAL ASP ASP SER SEQRES 13 A 161 VAL LYS ARG TYR LYS SEQRES 1 B 161 GLY SER HIS MET ILE GLN ALA TYR LEU GLY LEU GLY SER SEQRES 2 B 161 ASN ILE GLY ASP ARG GLU SER GLN LEU ASN ASP ALA ILE SEQRES 3 B 161 LYS ILE LEU ASN GLU TYR ASP GLY ILE SER VAL SER ASN SEQRES 4 B 161 ILE SER PRO ILE TYR GLU THR ALA PRO VAL GLY TYR THR SEQRES 5 B 161 GLU GLN PRO ASN PHE LEU ASN LEU CYS VAL GLU ILE GLN SEQRES 6 B 161 THR THR LEU THR VAL LEU GLN LEU LEU GLU CYS CYS LEU SEQRES 7 B 161 LYS THR GLU GLU CSO LEU HIS ARG ILE ARG LYS GLU ARG SEQRES 8 B 161 TRP GLY PRO ARG THR LEU ASP VAL ASP ILE LEU LEU TYR SEQRES 9 B 161 GLY GLU GLU MET ILE ASP LEU PRO LYS LEU SER VAL PRO SEQRES 10 B 161 HIS PRO ARG MET ASN GLU ARG ALA PHE VAL LEU ILE PRO SEQRES 11 B 161 LEU ASN ASP ILE ALA ALA ASN VAL VAL GLU PRO ARG SER SEQRES 12 B 161 LYS LEU LYS VAL LYS ASP LEU VAL PHE VAL ASP ASP SER SEQRES 13 B 161 VAL LYS ARG TYR LYS MODRES 5ETQ CSO A 80 CYS MODIFIED RESIDUE MODRES 5ETQ CSO B 80 CYS MODIFIED RESIDUE HET CSO A 80 7 HET CSO B 80 7 HET MG A 201 1 HET MG A 202 1 HET APC A 203 31 HET YH2 A 204 21 HET NA A 205 1 HET NA A 206 1 HET MG B 201 1 HET MG B 202 1 HET APC B 203 31 HET YH2 B 204 21 HET NA B 205 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MG MAGNESIUM ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM YH2 4-{[(2-AMINO-6-OXO-6,9-DIHYDRO-1H-PURIN-8-YL) HETNAM 2 YH2 SULFANYL]METHYL}BENZONITRILE HETNAM NA SODIUM ION HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 MG 4(MG 2+) FORMUL 5 APC 2(C11 H18 N5 O12 P3) FORMUL 6 YH2 2(C13 H10 N6 O S) FORMUL 7 NA 3(NA 1+) FORMUL 14 HOH *136(H2 O) HELIX 1 AA1 ASP A 14 TYR A 29 1 16 HELIX 2 AA2 THR A 66 LEU A 81 1 16 HELIX 3 AA3 ARG A 117 GLU A 120 5 4 HELIX 4 AA4 ARG A 121 ALA A 133 1 13 HELIX 5 AA5 VAL A 144 VAL A 148 1 5 HELIX 6 AA6 ASP B 14 TYR B 29 1 16 HELIX 7 AA7 THR B 66 LEU B 81 1 16 HELIX 8 AA8 ARG B 117 GLU B 120 5 4 HELIX 9 AA9 ARG B 121 ALA B 133 1 13 HELIX 10 AB1 VAL B 144 VAL B 148 1 5 SHEET 1 AA1 4 ILE A 32 ILE A 37 0 SHEET 2 AA1 4 PHE A 54 THR A 63 -1 O GLU A 60 N ASN A 36 SHEET 3 AA1 4 ILE A 2 SER A 10 -1 N ILE A 2 O THR A 63 SHEET 4 AA1 4 ASP A 95 TYR A 101 -1 O ASP A 97 N GLY A 7 SHEET 1 AA2 4 ILE A 32 ILE A 37 0 SHEET 2 AA2 4 PHE A 54 THR A 63 -1 O GLU A 60 N ASN A 36 SHEET 3 AA2 4 TYR A 41 THR A 43 -1 N TYR A 41 O ASN A 56 SHEET 4 AA2 4 VAL A 154 ARG A 156 -1 O LYS A 155 N GLU A 42 SHEET 1 AA3 2 ILE A 106 LEU A 108 0 SHEET 2 AA3 2 LEU A 111 VAL A 113 -1 O LEU A 111 N LEU A 108 SHEET 1 AA4 2 VAL A 136 GLU A 137 0 SHEET 2 AA4 2 LEU A 142 LYS A 143 -1 O LEU A 142 N GLU A 137 SHEET 1 AA5 4 ILE B 32 ILE B 37 0 SHEET 2 AA5 4 PHE B 54 THR B 63 -1 O GLU B 60 N ASN B 36 SHEET 3 AA5 4 ILE B 2 SER B 10 -1 N ILE B 2 O THR B 63 SHEET 4 AA5 4 ASP B 95 TYR B 101 -1 O ASP B 97 N GLY B 7 SHEET 1 AA6 4 ILE B 32 ILE B 37 0 SHEET 2 AA6 4 PHE B 54 THR B 63 -1 O GLU B 60 N ASN B 36 SHEET 3 AA6 4 TYR B 41 THR B 43 -1 N TYR B 41 O ASN B 56 SHEET 4 AA6 4 VAL B 154 ARG B 156 -1 O LYS B 155 N GLU B 42 SHEET 1 AA7 2 ILE B 106 LEU B 108 0 SHEET 2 AA7 2 LEU B 111 VAL B 113 -1 O LEU B 111 N LEU B 108 SHEET 1 AA8 2 VAL B 136 GLU B 137 0 SHEET 2 AA8 2 LEU B 142 LYS B 143 -1 O LEU B 142 N GLU B 137 LINK C GLU A 79 N CSO A 80 1555 1555 1.32 LINK C CSO A 80 N LEU A 81 1555 1555 1.31 LINK C GLU B 79 N CSO B 80 1555 1555 1.33 LINK C CSO B 80 N LEU B 81 1555 1555 1.32 LINK O ASN A 27 NA NA A 205 1555 1555 2.43 LINK O TYR A 29 NA NA A 205 1555 1555 2.41 LINK O ILE A 32 NA NA A 205 1555 1555 2.20 LINK OD2 ASP A 95 MG MG A 201 1555 1555 2.13 LINK OD1 ASP A 95 MG MG A 202 1555 1555 2.13 LINK OD2 ASP A 97 MG MG A 201 1555 1555 2.09 LINK OD1 ASP A 97 MG MG A 202 1555 1555 2.13 LINK OD1 ASP A 107 NA NA A 206 1555 1555 2.34 LINK MG MG A 201 O3G APC A 203 1555 1555 2.06 LINK MG MG A 201 O2B APC A 203 1555 1555 2.02 LINK MG MG A 201 O HOH A 342 1555 1555 2.07 LINK MG MG A 201 O HOH A 355 1555 1555 2.16 LINK MG MG A 202 O2B APC A 203 1555 1555 2.16 LINK MG MG A 202 O2A APC A 203 1555 1555 2.04 LINK MG MG A 202 O HOH A 310 1555 1555 2.04 LINK MG MG A 202 O HOH A 327 1555 1555 2.02 LINK NA NA A 205 O HOH A 315 1555 1555 2.39 LINK NA NA A 205 O HOH A 370 1555 1555 2.42 LINK NA NA A 205 O HOH B 358 1555 1656 2.32 LINK NA NA A 206 O HOH A 333 1555 1555 2.22 LINK NA NA A 206 OD1 ASP B 107 1555 1555 2.29 LINK NA NA A 206 O HOH B 311 1555 1555 2.10 LINK NA NA A 206 O HOH B 332 1555 1555 2.12 LINK O HOH A 315 NA NA B 205 1454 1555 2.38 LINK O HOH A 370 NA NA B 205 1454 1555 2.38 LINK O ASN B 27 NA NA B 205 1555 1555 2.36 LINK O TYR B 29 NA NA B 205 1555 1555 2.56 LINK O ILE B 32 NA NA B 205 1555 1555 2.22 LINK OD1 ASP B 95 MG MG B 201 1555 1555 2.13 LINK OD2 ASP B 95 MG MG B 202 1555 1555 2.19 LINK OD1 ASP B 97 MG MG B 201 1555 1555 2.12 LINK OD2 ASP B 97 MG MG B 202 1555 1555 2.16 LINK MG MG B 201 O2B APC B 203 1555 1555 2.06 LINK MG MG B 201 O1A APC B 203 1555 1555 2.03 LINK MG MG B 201 O HOH B 309 1555 1555 2.10 LINK MG MG B 201 O HOH B 341 1555 1555 2.11 LINK MG MG B 202 O1G APC B 203 1555 1555 2.02 LINK MG MG B 202 O2B APC B 203 1555 1555 2.10 LINK MG MG B 202 O HOH B 329 1555 1555 2.09 LINK MG MG B 202 O HOH B 348 1555 1555 2.09 LINK NA NA B 205 O HOH B 358 1555 1555 2.40 CISPEP 1 VAL A 113 PRO A 114 0 -5.93 CISPEP 2 VAL B 113 PRO B 114 0 -6.80 SITE 1 AC1 6 ASP A 95 ASP A 97 MG A 202 APC A 203 SITE 2 AC1 6 HOH A 342 HOH A 355 SITE 1 AC2 6 ASP A 95 ASP A 97 MG A 201 APC A 203 SITE 2 AC2 6 HOH A 310 HOH A 327 SITE 1 AC3 24 LEU A 71 ARG A 83 ARG A 85 ARG A 92 SITE 2 AC3 24 ASP A 95 ASP A 97 ILE A 98 LYS A 110 SITE 3 AC3 24 LEU A 111 SER A 112 HIS A 115 ARG A 117 SITE 4 AC3 24 ARG A 121 MG A 201 MG A 202 YH2 A 204 SITE 5 AC3 24 HOH A 301 HOH A 303 HOH A 310 HOH A 311 SITE 6 AC3 24 HOH A 327 HOH A 342 HOH A 348 HOH A 355 SITE 1 AC4 16 ASN A 11 THR A 43 ALA A 44 PRO A 45 SITE 2 AC4 16 VAL A 46 GLN A 51 PHE A 54 ASN A 56 SITE 3 AC4 16 GLY A 90 PRO A 91 ARG A 92 ARG A 121 SITE 4 AC4 16 PHE A 123 APC A 203 HOH A 342 HOH A 360 SITE 1 AC5 7 ASN A 27 TYR A 29 ILE A 32 HOH A 315 SITE 2 AC5 7 HOH A 370 NA B 205 HOH B 358 SITE 1 AC6 5 ASP A 107 HOH A 333 ASP B 107 HOH B 311 SITE 2 AC6 5 HOH B 332 SITE 1 AC7 6 ASP B 95 ASP B 97 MG B 202 APC B 203 SITE 2 AC7 6 HOH B 309 HOH B 341 SITE 1 AC8 6 ASP B 95 ASP B 97 MG B 201 APC B 203 SITE 2 AC8 6 HOH B 329 HOH B 348 SITE 1 AC9 21 LEU B 71 ARG B 83 ARG B 92 ASP B 95 SITE 2 AC9 21 ASP B 97 ILE B 98 LYS B 110 LEU B 111 SITE 3 AC9 21 SER B 112 HIS B 115 ARG B 117 ARG B 121 SITE 4 AC9 21 MG B 201 MG B 202 HOH B 301 HOH B 309 SITE 5 AC9 21 HOH B 313 HOH B 329 HOH B 341 HOH B 348 SITE 6 AC9 21 HOH B 353 SITE 1 AD1 15 ASN B 11 THR B 43 ALA B 44 PRO B 45 SITE 2 AD1 15 VAL B 46 GLN B 51 PHE B 54 ASN B 56 SITE 3 AD1 15 GLY B 90 PRO B 91 ARG B 92 ARG B 121 SITE 4 AD1 15 PHE B 123 HOH B 329 HOH B 347 SITE 1 AD2 7 NA A 205 HOH A 315 HOH A 370 ASN B 27 SITE 2 AD2 7 TYR B 29 ILE B 32 HOH B 358 CRYST1 47.630 68.200 52.820 90.00 106.05 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 0.020995 0.000000 0.006040 0.00000 SCALE2 0.000000 0.014663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019700 0.00000