OCA Atlas for 6QTK

6QTK

Isomerase

date

Feb 25, 2019

title

2.31a Structure Of Gepotidacin With S.Aureus Dna Gyrase And Nicked Dna

authors

B.D.Bax

compound

source

Molecule: Dna Gyrase Subunit B
Chain: B, D
Ec: 5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus (Strain N315)
Organism_taxid: 158879
Strain: N315
Gene: Gyrb, Sa0005
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Gyrase Subunit A
Chain: A, C
Ec: 5.99.1.3
Engineered: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apgpcpcpgptpapggpgptpapcpcptpapcpgpgp
Chain: E, F
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630

symmetry

Space Group: P 61

R_factor

0.163

R_Free

0.203

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
92.730	92.730	408.775	90.00	90.00	120.00

method

X-Ray Diffraction

resolution

2.31 Å

ligand

GOL, JHN, MN, NA

enzyme

Isomerase E.C.5.99.1.3 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, C
D, B

Primary reference

Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase., Gibson EG, Bax B, Chan PF, Osheroff N, ACS Infect Dis. 2019 Feb 28. doi: 10.1021/acsinfecdis.8b00315. PMID:30757898

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (260 Kb) [Save to disk]

Biological Unit Coordinates (6qtk.pdb1.gz) 251 Kb

LPC: Ligand-Protein Contacts for 6QTK

CSU: Contacts of Structural Units for 6QTK

Structure Factors (855 Kb)

Retrieve 6QTK in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 6QTK from S2C, [Save to disk]

View 6QTK in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 6QTK

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [6qtk_A] [6qtk_F] [6qtk_B] [6qtk_E] [6qtk_D] [6qtk_C]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 6QTK

Community annotation for 6QTK at PDBWiki (http://pdbwiki.org)

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