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Crystal structure of the ATPase region of mycobacterium tuberculosis gyrb with amppnp
Analyse Crystal structure of the ATPase region of mycobacterium tuberculosis gyrb with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZKD
- Type
- protein
- Length
- 3,035 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- I6WX66
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 377 | 37% helix, 26% strand | I6WX66 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 375 | 35% helix, 26% strand | I6WX66 |
| C | DNA gyrase subunit B (EC 5.99.1.3) | protein | 390 | 37% helix, 27% strand | I6WX66 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 379 | 36% helix, 27% strand | I6WX66 |
| E | DNA gyrase subunit B (EC 5.99.1.3) | protein | 382 | 33% helix, 27% strand | I6WX66 |
| F | DNA gyrase subunit B (EC 5.99.1.3) | protein | 376 | 36% helix, 27% strand | I6WX66 |
| G | DNA gyrase subunit B (EC 5.99.1.3) | protein | 378 | 34% helix, 27% strand | I6WX66 |
| H | DNA gyrase subunit B (EC 5.99.1.3) | protein | 378 | 35% helix, 26% strand | I6WX66 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.82 | 0.98 | 35 | ANP, MG |
| 2 | 150 | 0.82 | 0.98 | 36 | ANP, MG |
| 3 | 157 | 0.82 | 0.98 | 36 | ANP, MG |
| 4 | 142 | 0.82 | 0.98 | 30 | ANP |
| 5 | 918 | 0.81 | 0.83 | 92 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2567 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2499 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2364 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2267 Ų buried · 38 hydrogen bonds · protein-protein
- C–G · 834 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ZKD · CRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
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 I6WX66
- Elsewhere: RCSB PDB 3ZKD · PDBe 3ZKD · UniProt I6WX66
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