Research workbench
M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin
Analyse M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UGW
- Type
- protein + DNA
- Length
- 1,510 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B; DNA (46-mer); Evybactin
- EC
- 5.6.2.2
- UniProt
- P9WG47, P9WG45
- Ligands
- MG
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.6.2.2) | protein | 485 | 49% helix, 19% strand | P9WG47 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 248 | 40% helix, 15% strand | P9WG45 |
| C | DNA gyrase subunit a (EC 5.6.2.2) | protein | 487 | 50% helix, 17% strand | P9WG47 |
| D | DNA gyrase subunit B (EC 5.6.2.2) | protein | 232 | 42% helix, 13% strand | P9WG45 |
| V | DNA (46-mer) | dna | 46 | — | — |
| E | Evybactin | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.84 | 0.87 | 82 | MG |
| 2 | 796 | 0.78 | 0.82 | 62 | empty |
| 3 | 765 | 0.78 | 0.82 | 63 | empty |
| 4 | 405 | 0.70 | 0.82 | 42 | empty |
| 5 | 292 | 0.68 | 0.83 | 44 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1826 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1719 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1529 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 992 Ų buried · 13 hydrogen bonds · protein-protein
- C–V · 983 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified, 3 d-amino (D-amino acid, nonstandard, methylation).
Compared structures
- 7UGW · M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin · the same entry in another collection · chain V against V, TM-score 1.00
- P9WG47 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P9WG47) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P9WG45 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P9WG45) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P9WG47
- Every structure of UniProt P9WG45
- Elsewhere: RCSB PDB 7UGW · PDBe 7UGW · UniProt P9WG47 · UniProt P9WG45
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