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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYRB COMPLEXED WITH A FRAGMENT
 
Authors :  O. A. Andersen, J. Barker, R. K. Cheng, J. Kahmann, B. Felicetti, M. Wood C. Scheich, M. Mesleh, J. B. Cross, J. Zhang, Q. Yang, B. Lippa, M. D. Rya
Date :  21 Jul 15  (Deposition) - 03 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Gyrase, Gyrb, Fragment-Based Screening, Structure-Based Design, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Mesleh, J. B. Cross, J. Zhang, J. Kahmann, O. A. Andersen, J. Barker, R. K. Cheng, B. Felicetti, M. Wood, A. T. Hadfield, C. Scheich, T. I. Moy, Q. Yang, J. Shotwell, K. Nguyen, B. Lippa, R. Dolle, M. D. Ryan
Fragment-Based Discovery Of Dna Gyrase Inhibitors Targeting The Atpase Subunit Of Gyrb.
Bioorg. Med. Chem. Lett. V. 26 1314 2016
PubMed-ID: 26786695  |  Reference-DOI: 10.1016/J.BMCL.2016.01.009

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ATP BINDING DOMAIN, UNP RESIDUES 2-234 (DELTA 105-127)
    Gene: GYRB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EVO2Ligand/Ion(3E)-3-(PYRIDIN-3-YLMETHYLIDENE)-1,3-DIHYDRO-2H-INDOL-2-ONE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EVO1Ligand/Ion(3E)-3-(PYRIDIN-3-YLMETHYLIDENE)-1,3-DIHYDRO-2H-INDOL-2-ONE
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EVO1Ligand/Ion(3E)-3-(PYRIDIN-3-YLMETHYLIDENE)-1,3-DIHYDRO-2H-INDOL-2-ONE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , GLU A:58 , ASP A:81 , ILE A:86 , ILE A:102 , ILE A:175 , HOH A:427 , HOH A:446binding site for residue EVO A 301
2AC2SOFTWARETHR A:80 , ASP A:81 , HIS A:143 , LYS A:170 , THR A:171 , GLY A:172 , HOH A:443 , HOH A:499binding site for residue SO4 A 302
3AC3SOFTWAREHIS B:143 , VAL B:174 , GLU B:186 , THR B:187 , HOH B:479 , HOH B:535 , HOH B:579binding site for residue MPD B 301
4AC4SOFTWAREASN B:54 , GLU B:58 , ASP B:81 , ILE B:86 , ILE B:102 , HOH B:455 , HOH B:586binding site for residue EVO B 302
5AC5SOFTWARETHR B:80 , ASP B:81 , HIS B:143 , LYS B:170 , THR B:171 , GLY B:172 , THR B:173 , HOH B:410 , HOH B:479binding site for residue SO4 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CPH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CPH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CPH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CPH)

(-) Exons   (0, 0)

(no "Exon" information available for 5CPH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cph A  16 AGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    25        35        45        55        65        75        85        95       128       138       148       158       168       178       188       198       208       218       228  
                                                                                                                  104|                                                                                                      
                                                                                                                   128                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee............hhhhhhhh.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cph B  20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    29        39        49        59        69        79        89 ||    102 ||    135       145       155       165       175       185       195       205       215       225      
                                                                                                  91|      104|                                                                                                       
                                                                                                   95       128
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CPH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CPH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CPH)

(-) Gene Ontology  (13, 13)

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  GYRB_STAAU | P0A0K8
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  5.99.1.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GYRB_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 4uro 5bs3 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

5ctu 5ctx 5cty 5cuw