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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 :  13 Aug 15  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
157X2Ligand/Ion7-PROPYL-3-[2-(PYRIDIN-3-YL)-1,3-THIAZOL-5-YL]-1,7-DIHYDRO-6H-PYRAZOLO[3,4-B]PYRIDIN-6-ONE
2CL2Ligand/IonCHLORIDE ION
3MG7Ligand/IonMAGNESIUM ION
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
157X1Ligand/Ion7-PROPYL-3-[2-(PYRIDIN-3-YL)-1,3-THIAZOL-5-YL]-1,7-DIHYDRO-6H-PYRAZOLO[3,4-B]PYRIDIN-6-ONE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
157X1Ligand/Ion7-PROPYL-3-[2-(PYRIDIN-3-YL)-1,3-THIAZOL-5-YL]-1,7-DIHYDRO-6H-PYRAZOLO[3,4-B]PYRIDIN-6-ONE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:81 , HIS A:143 , LYS A:170 , THR A:171 , MPD A:302 , HOH A:413binding site for residue MPD A 301
02AC2SOFTWARETYR A:141 , HIS A:143 , MPD A:301binding site for residue MPD A 302
03AC3SOFTWAREVAL A:88 , ARG A:144 , ASN A:145 , HOH A:523binding site for residue CL A 303
04AC4SOFTWAREASP A:57 , MG A:305 , HOH A:446 , HOH A:516binding site for residue MG A 304
05AC5SOFTWAREASP A:53 , ASN A:54 , ASP A:57 , MG A:304 , MG A:306 , HOH A:446 , HOH A:469 , HOH A:499 , HOH A:531binding site for residue MG A 305
06AC6SOFTWAREGLU A:50 , MG A:305 , HOH A:469 , HOH A:499 , HOH A:521 , HOH A:531binding site for residue MG A 306
07AC7SOFTWAREASN 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:442binding site for residue 57X A 307
08AC8SOFTWARELYS A:163 , HOH A:450 , HOH A:475 , ASP B:53 , ASP B:57binding site for residue MG A 300
09AC9SOFTWARETHR B:80 , ASP B:81 , LYS B:170 , MPD B:303 , HOH B:416binding site for residue MPD B 302
10AD1SOFTWAREHIS B:143 , VAL B:174 , GLU B:186 , MPD B:302 , HOH B:486binding site for residue MPD B 303
11AD2SOFTWAREVAL B:88 , ASP B:89 , ARG B:144 , ASN B:145 , HOH B:455binding site for residue CL B 304
12AD3SOFTWAREASN B:54 , HOH B:408 , HOH B:449 , HOH B:492 , HOH B:493 , HOH B:540binding site for residue MG B 305
13AD4SOFTWAREASN B:82 , GLY B:83 , THR B:171 , HOH B:467 , HOH B:479 , HOH B:508 , HOH B:510binding site for residue MG B 306
14AD5SOFTWAREGLY B:208 , HIS B:228 , HOH B:462 , HOH B:483 , HOH B:521 , HOH B:524binding site for residue MG B 307
15AD6SOFTWARETHR A:185 , 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:435 , HOH B:502binding site for residue 57X B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7D)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7D)

(-) 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........ee....eehhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7d 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:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7d B  20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    29        39        49        59        69        79        89        99    || 132       142       152       162       172       182       192       202       212       222         
                                                                                                              104|                                                                                                       
                                                                                                               128
   Legend:   → Mismatch (orange background)
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    → 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 5D7D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7D)

(-) Gene Ontology  (13, 13)

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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 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7r