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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYRB COMPLEXED WITH A LIGAND
 
Authors :  J. Zhang, Q. Yang, J. B. Cross, J. A. C. Romero, M. D. Ryan, B. Lippa, R. E. D O. A. Andersen, J. Barker, R. K. Cheng, J. Kahmann, B. Felicetti, M. Woo C. Scheich
Date :  12 Aug 15  (Deposition) - 25 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Gyrase, Gyrb, Ligand, Structure-Based Design, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, Q. Yang, J. B. Cross, J. A. Romero, K. M. Poutsiaka, F. Epie, D. Bevan, B. Wang, Y. Zhang, A. Chavan, X. Zhang, T. Moy, A. Daniel, K. Nguyen, B. Chamberlain, N. Carter, J. Shotwell, J. Silverman, C. A. Metcalf, D. Ryan, B. Lippa, R. E. Dolle
Discovery Of Azaindole Ureas As A Novel Class Of Bacterial Gyrase B Inhibitors.
J. Med. Chem. V. 58 8503 2015
PubMed-ID: 26460684  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00961

(-) 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
157U2Ligand/Ion1-ETHYL-3-[4-(HYDROXYMETHYL)-5-(1H-PYRROL-2-YL)-1,3-THIAZOL-2-YL]UREA
2GOL1Ligand/IonGLYCEROL
3MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
157U1Ligand/Ion1-ETHYL-3-[4-(HYDROXYMETHYL)-5-(1H-PYRROL-2-YL)-1,3-THIAZOL-2-YL]UREA
2GOL1Ligand/IonGLYCEROL
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
157U1Ligand/Ion1-ETHYL-3-[4-(HYDROXYMETHYL)-5-(1H-PYRROL-2-YL)-1,3-THIAZOL-2-YL]UREA
2GOL-1Ligand/IonGLYCEROL
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:51 , ASN A:54 , SER A:55 , GLU A:58 , VAL A:79 , ASP A:81 , ARG A:84 , GLY A:85 , ILE A:86 , PRO A:87 , ILE A:102 , THR A:173 , GOL A:303 , HOH A:424binding site for residue 57U A 301
2AC2SOFTWARETHR A:80 , ASP A:81 , HIS A:143 , THR A:171 , GLY A:172binding site for residue MPD A 302
3AC3SOFTWAREILE A:51 , ASN A:54 , ILE A:102 , SER A:129 , 57U A:301binding site for residue GOL A 303
4AC4SOFTWAREILE B:51 , ASN B:54 , SER B:55 , GLU B:58 , VAL B:79 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , ILE B:102 , ILE B:175 , HOH B:414 , HOH B:454binding site for residue 57U B 301
5AC5SOFTWAREHIS B:143 , LYS B:170 , MPD B:303binding site for residue MPD B 302
6AC6SOFTWAREHIS B:143 , GLU B:186 , VAL B:189 , MPD B:302binding site for residue MPD B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D6P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D6P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D6P)

(-) Exons   (0, 0)

(no "Exon" information available for 5D6P)

(-) 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....eeeeee.hhh.eeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d6p 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh.eeeee............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d6p B  20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGG 232
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5D6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D6P)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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  GYRB_STAAU | P0A0K8
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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 5cph 5ctu 5ctw 5ctx 5cty 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

5cph 5ctu 5ctw 5ctx 5cty 5d6q