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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 :  14 Aug 15  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
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. A. Romero, J. Cross, B. Wang, K. M. Poutsiaka, F. Epie, D. Bevan, Y. Wu, T. Moy, A. Daniel, B. Chamberlain, N. Carter, J. Shotwell, A. Arya, V. Kumar, J. Silverman, K. Nguyen, C. A. Metcalf, D. Ryan, B. Lippa, R. E. Dolle
Discovery Of Indazole Derivatives As A Novel Class Of Bacterial Gyrase B Inhibitors.
Acs Med. Chem. Lett. V. 6 1080 2015
PubMed-ID: 26487916  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00266

(-) 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
157Y2Ligand/Ion3-HYDROXY-5-[5-(6-HYDROXY-7-PROPYL-2H-INDAZOL-3-YL)-1,3-THIAZOL-2-YL]PYRIDINE-2-CARBOXYLIC ACID
2CL2Ligand/IonCHLORIDE ION
3MG8Ligand/IonMAGNESIUM ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
157Y1Ligand/Ion3-HYDROXY-5-[5-(6-HYDROXY-7-PROPYL-2H-INDAZOL-3-YL)-1,3-THIAZOL-2-YL]PYRIDINE-2-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
157Y1Ligand/Ion3-HYDROXY-5-[5-(6-HYDROXY-7-PROPYL-2H-INDAZOL-3-YL)-1,3-THIAZOL-2-YL]PYRIDINE-2-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:53 , ASN A:54 , ASP A:57 , MG A:302 , HOH A:409 , HOH A:470 , HOH A:503 , HOH A:521binding site for residue MG A 301
02AC2SOFTWAREGLU A:50 , MG A:301 , HOH A:449 , HOH A:470 , HOH A:503 , HOH A:521binding site for residue MG A 302
03AC3SOFTWAREASP A:57 , HOH A:409 , HOH A:524binding site for residue MG A 303
04AC4SOFTWAREGLY A:208 , HIS A:228 , HOH A:505 , HOH A:506binding site for residue MG A 304
05AC5SOFTWAREVAL A:88 , ARG A:144 , ASN A:145binding site for residue CL A 305
06AC6SOFTWAREILE 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 , ARG A:144 , THR A:173 , ILE A:175 , HOH A:406 , HOH A:408 , HOH A:432 , HOH A:443 , HOH A:537binding site for residue 57Y A 306
07AC7SOFTWAREASN B:54 , HOH B:409 , HOH B:429 , HOH B:506 , HOH B:533binding site for residue MG B 301
08AC8SOFTWAREGLY B:208 , HIS B:228 , HOH B:490 , HOH B:496 , HOH B:534binding site for residue MG B 302
09AC9SOFTWAREGLU B:164 , GLU B:219 , HOH B:461 , HOH B:487binding site for residue MG B 303
10AD1SOFTWAREASN B:82 , GLY B:83 , THR B:171 , HOH B:467 , HOH B:520binding site for residue MG B 304
11AD2SOFTWAREHIS B:143 , VAL B:174 , GLU B:186 , HOH B:485binding site for residue MPD B 305
12AD3SOFTWAREVAL B:88 , ASP B:89 , ARG B:144 , ASN B:145binding site for residue CL B 306
13AD4SOFTWARETHR A:185 , GLU A:186 , HOH A:450 , 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 , ARG B:144 , THR B:173 , ILE B:175 , HOH B:401 , HOH B:402 , HOH B:403 , HOH B:404 , HOH B:413 , HOH B:432 , HOH B:434 , HOH B:454 , HOH B:509 , HOH B:510binding site for residue 57Y B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7R)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7R)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7r A  15 GAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    24        34        44        54        64        74        84        94       104|      137       147       157       167       177       187       197       207       217       227   
                                                                                                                   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 .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7r B  19 IQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    28        38        48        58        68        78        88  ||   101  ||   134       144       154       164       174       184       194       204       214       224       
                                                                                                   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 5D7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7R)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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  GYRB_STAAU | P0A0K8
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 Related Entries

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

(-) Related Entries Specified in the PDB File

5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d