Research workbench
2.5A structure of GSK945237 with S.AUREUS DNA gyrase and DNA.
Analyse 2.5A structure of GSK945237 with S.AUREUS DNA gyrase and DNA. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IWM
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit B; DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- 6EJ, MN
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 47% helix, 12% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 483 | 47% helix, 18% strand | Q99XG5 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 48% helix, 17% strand | Q99XG5 |
| E | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*TP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*AP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 20 | — | — |
Ligands and binding sites
- 6EJ · (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one · ligand · chains A, C, E, F
- MN · Manganese (II) ion · metal · 2 copies · chains B, E, D, F
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.77 | 0.84 | 50 | 6EJ |
| 2 | 493 | 0.76 | 0.84 | 37 | empty |
| 3 | 386 | 0.70 | 0.82 | 33 | empty |
| 4 | 256 | 0.68 | 0.85 | 34 | empty |
| 5 | 211 | 0.67 | 0.85 | 28 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1719 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 1505 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1493 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1049 Ų buried · 131 hydrogen bonds · nucleic-nucleic
- A–D · 723 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5IWM · 2.5A structure of GSK945237 with S.aureus DNA gyrase and DNA. · the same entry in another collection · chain F against F, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 5IWM · PDBe 5IWM · UniProt P66937 · UniProt Q99XG5
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