MolNFT v1 · #122677 · protein + DNA
1.98A structure of GSK945237 with S.AUREUS DNA gyrase and singly nicked DNA
5IWI · DNA gyrase subunit B,DNA gyrase subunit B: “1.98A structure of GSK945237 with S.AUREUS DNA gyrase and singly nicked DNA”. X-ray diffraction, 3 ligands (6EJ, MN, CL), 17 pockets (best druggability 0.85). MolNFT v1 #122677 on…
- PDB
- 5IWI
- Type
- protein + DNA
- Length
- 1,384 residues
- Chains
- 7
- 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, CL
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 192 | 48% helix, 11% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 483 | 49% helix, 18% strand | Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 48% helix, 13% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 18% strand | Q99XG5 |
| E | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 8 | — | — |
| G | DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 11 | — | — |
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, G
- MN · Manganese (II) ion · metal · 3 copies · chains B, E, D, F, C
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 10 copies · chains A, E, C, F
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 | 1121 | 0.85 | 0.86 | 130 | GOL, 6EJ |
| 2 | 436 | 0.74 | 0.84 | 36 | empty |
| 3 | 396 | 0.70 | 0.82 | 31 | empty |
| 4 | 273 | 0.63 | 0.81 | 40 | empty |
| 5 | 489 | 0.62 | 0.76 | 52 | GOL |
Interfaces
19 interfaces between chains.
- A–C · 1759 Ų buried · 26 hydrogen bonds · protein-protein
- B–A · 1518 Ų buried · 14 hydrogen bonds · protein-protein
- D–C · 1477 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 718 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 662 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5IWI · 1.98A structure of GSK945237 with S.aureus DNA gyrase and singly nicked DNA · the same entry in another collection · chain G against G, TM-score 1.00
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain D against A, TM-score 0.98
- 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
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 5IWI · PDBe 5IWI · UniProt P66937 · UniProt Q99XG5
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