HEADER HYDROLASE 15-MAR-19 6R1V TITLE SOLUTION STRUCTURE OF SORTASE A FROM S. AUREUS IN COMPLEX WITH 2- TITLE 2 (AMINOMETHYL)-3-HYDROXY-4H-PYRAN-4-ONE BASED PRODRUG COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SURFACE PROTEIN SORTING A; COMPND 5 EC: 3.4.22.70; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325; SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 GENE: SRTA, SAOUHSC_02834; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS INHIBITOR, COVALENT COMPLEX, PRODRUG, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.JAUDZEMS,A.LEONCHIKS REVDAT 3 14-JUN-23 6R1V 1 REMARK REVDAT 2 26-FEB-20 6R1V 1 JRNL REVDAT 1 22-JAN-20 6R1V 0 JRNL AUTH K.JAUDZEMS,V.KURBATSKA,A.JE KABSONS,R.BOBROVS,Z.RUDEVICA, JRNL AUTH 2 A.LEONCHIKS JRNL TITL TARGETING BACTERIAL SORTASE A WITH COVALENT INHIBITORS: 27 JRNL TITL 2 NEW STARTING POINTS FOR STRUCTURE-BASED HIT-TO-LEAD JRNL TITL 3 OPTIMIZATION. JRNL REF ACS INFECT DIS. V. 6 186 2020 JRNL REFN ESSN 2373-8227 JRNL PMID 31724850 JRNL DOI 10.1021/ACSINFECDIS.9B00265 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, CYANA 2.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6R1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101101. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM [U-13C; U-15N] SORTASE A REMARK 210 PROTEIN, 3.2 MM 3-HYDROXY-6-(HYDROXYMETHYL)-2-(THIOPHEN-3- REMARK 210 YLMETHYL)-4H-PYRAN-4-ONE, 20 MM SODIUM ACETATE, 50 MM SODIUM REMARK 210 CHLORIDE, 10 MM CALCIUM CHLORIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D (F1)-15N,13C- REMARK 210 FILTERED 1H-13C NOESY ALIPHATIC; REMARK 210 2D (F1,F2)-13C,15N-FILTERED REMARK 210 TOCSY; 2D (F1,F2)-13C,15N- REMARK 210 FILTERED NOESY; 2D 1H-15N HSQC; REMARK 210 3D HNCA; 3D CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TOPSPIN, VNMR 2.1B, CARA REMARK 210 1.9, UNIO REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HH11 ARG A 139 O2 JPT A 201 1.54 REMARK 500 OD2 ASP A 118 HZ3 LYS A 119 1.55 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 1 LYS A 4 94.69 54.60 REMARK 500 1 PRO A 33 31.75 -87.58 REMARK 500 1 TYR A 70 -161.16 -119.33 REMARK 500 1 GLN A 71 -77.76 -60.21 REMARK 500 1 MET A 83 85.34 50.56 REMARK 500 1 ASN A 90 -38.59 -169.11 REMARK 500 1 VAL A 103 -169.16 -126.41 REMARK 500 1 GLN A 114 47.88 -86.30 REMARK 500 1 ASP A 118 -157.32 -89.62 REMARK 500 1 ASP A 128 98.97 70.14 REMARK 500 2 ALA A 34 75.44 65.15 REMARK 500 2 ASN A 69 84.49 -155.64 REMARK 500 2 TYR A 70 -168.87 -108.56 REMARK 500 2 PHE A 72 78.81 -114.41 REMARK 500 2 ASN A 74 30.62 -87.17 REMARK 500 2 LYS A 79 -169.08 -111.54 REMARK 500 2 MET A 83 76.01 50.17 REMARK 500 2 LYS A 117 176.64 -59.84 REMARK 500 2 ASP A 128 82.28 62.21 REMARK 500 3 GLN A 2 -170.25 -69.84 REMARK 500 3 LYS A 26 29.77 -143.57 REMARK 500 3 PRO A 33 30.63 -82.44 REMARK 500 3 ALA A 34 82.90 61.85 REMARK 500 3 GLN A 71 -77.20 -43.55 REMARK 500 3 PHE A 72 79.66 -106.20 REMARK 500 3 MET A 83 78.01 49.70 REMARK 500 3 ASP A 118 -154.74 -94.56 REMARK 500 3 THR A 133 -34.81 -141.20 REMARK 500 3 GLU A 137 -74.72 -77.60 REMARK 500 4 PRO A 33 30.99 -79.19 REMARK 500 4 TYR A 70 -160.25 -126.76 REMARK 500 4 GLN A 71 -78.61 -59.44 REMARK 500 4 PHE A 72 31.66 -91.09 REMARK 500 4 MET A 83 90.43 57.01 REMARK 500 4 ASP A 118 -158.62 -95.81 REMARK 500 5 LYS A 4 93.77 53.94 REMARK 500 5 PRO A 33 30.02 -88.18 REMARK 500 5 ASN A 49 31.05 -85.47 REMARK 500 5 TYR A 70 -157.79 -99.12 REMARK 500 5 GLN A 71 -75.47 -43.57 REMARK 500 5 PHE A 72 77.17 -100.03 REMARK 500 5 THR A 73 -52.03 -137.84 REMARK 500 5 MET A 83 83.30 53.91 REMARK 500 5 ASN A 90 11.07 -148.18 REMARK 500 5 ARG A 101 -166.58 -165.23 REMARK 500 5 ASP A 118 -156.25 -85.13 REMARK 500 5 ASP A 127 76.73 -110.54 REMARK 500 5 ASP A 128 -80.38 -162.88 REMARK 500 5 TYR A 129 86.67 61.03 REMARK 500 6 LYS A 26 45.73 -156.41 REMARK 500 REMARK 500 THIS ENTRY HAS 189 RAMACHANDRAN OUTLIERS. 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 JPT A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34379 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF SORTASE A FROM S. AUREUS IN COMPLEX WITH 2- REMARK 900 (AMINOMETHYL)-3-HYDROXY-4H-PYRAN-4-ONE BASED PRODRUG DBREF 6R1V A 2 148 UNP Q2FV99 SRTA_STAA8 60 206 SEQADV 6R1V MET A 1 UNP Q2FV99 INITIATING METHIONINE SEQADV 6R1V GLU A 109 UNP Q2FV99 GLY 167 CONFLICT SEQRES 1 A 148 MET GLN ALA LYS PRO GLN ILE PRO LYS ASP LYS SER LYS SEQRES 2 A 148 VAL ALA GLY TYR ILE GLU ILE PRO ASP ALA ASP ILE LYS SEQRES 3 A 148 GLU PRO VAL TYR PRO GLY PRO ALA THR PRO GLU GLN LEU SEQRES 4 A 148 ASN ARG GLY VAL SER PHE ALA GLU GLU ASN GLU SER LEU SEQRES 5 A 148 ASP ASP GLN ASN ILE SER ILE ALA GLY HIS THR PHE ILE SEQRES 6 A 148 ASP ARG PRO ASN TYR GLN PHE THR ASN LEU LYS ALA ALA SEQRES 7 A 148 LYS LYS GLY SER MET VAL TYR PHE LYS VAL GLY ASN GLU SEQRES 8 A 148 THR ARG LYS TYR LYS MET THR SER ILE ARG ASP VAL LYS SEQRES 9 A 148 PRO THR ASP VAL GLU VAL LEU ASP GLU GLN LYS GLY LYS SEQRES 10 A 148 ASP LYS GLN LEU THR LEU ILE THR CYS ASP ASP TYR ASN SEQRES 11 A 148 GLU LYS THR GLY VAL TRP GLU LYS ARG LYS ILE PHE VAL SEQRES 12 A 148 ALA THR GLU VAL LYS HET JPT A 201 25 HETNAM JPT 6-(HYDROXYMETHYL)-3-OXIDANYL-2-(THIOPHEN-3-YLMETHYL) HETNAM 2 JPT PYRAN-4-ONE FORMUL 2 JPT C11 H10 O4 S HELIX 1 AA1 PRO A 21 ASP A 24 5 4 HELIX 2 AA2 THR A 35 GLY A 42 1 8 HELIX 3 AA3 ASN A 74 ALA A 78 5 5 SHEET 1 AA1 9 GLY A 16 ILE A 20 0 SHEET 2 AA1 9 ILE A 25 TYR A 30 -1 O GLU A 27 N ILE A 18 SHEET 3 AA1 9 VAL A 43 PHE A 45 1 O VAL A 43 N TYR A 30 SHEET 4 AA1 9 ASN A 56 HIS A 62 -1 O ALA A 60 N SER A 44 SHEET 5 AA1 9 GLN A 120 TYR A 129 1 O ILE A 124 N GLY A 61 SHEET 6 AA1 9 TRP A 136 GLU A 146 -1 O LYS A 138 N ASP A 127 SHEET 7 AA1 9 GLU A 91 VAL A 103 -1 N ARG A 101 O ILE A 141 SHEET 8 AA1 9 VAL A 84 VAL A 88 -1 N PHE A 86 O ARG A 93 SHEET 9 AA1 9 GLY A 16 ILE A 20 -1 N GLU A 19 O TYR A 85 LINK SG CYS A 126 C7 JPT A 201 1555 1555 1.78 SITE 1 AC1 5 ALA A 60 ILE A 124 CYS A 126 TRP A 136 SITE 2 AC1 5 ARG A 139 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1