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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
- 3ZKB
- Type
- protein
- Length
- 6,098 residues
- Chains
- 16
- 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 0.83
Structure
x-ray diffraction · 16 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 380 | 36% helix, 26% strand | I6WX66 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 382 | 36% helix, 24% strand | I6WX66 |
| C | DNA gyrase subunit B (EC 5.99.1.3) | protein | 387 | 35% helix, 26% strand | I6WX66 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 392 | 35% helix, 26% strand | I6WX66 |
| E | DNA gyrase subunit B (EC 5.99.1.3) | protein | 386 | 36% helix, 26% strand | I6WX66 |
| F | DNA gyrase subunit B (EC 5.99.1.3) | protein | 383 | 36% helix, 25% strand | I6WX66 |
| G | DNA gyrase subunit B (EC 5.99.1.3) | protein | 381 | 35% helix, 26% strand | I6WX66 |
| H | DNA gyrase subunit B (EC 5.99.1.3) | protein | 379 | 35% helix, 26% strand | I6WX66 |
| I | DNA gyrase subunit B (EC 5.99.1.3) | protein | 375 | 35% helix, 27% strand | I6WX66 |
| J | DNA gyrase subunit B (EC 5.99.1.3) | protein | 384 | 35% helix, 26% strand | I6WX66 |
| K | DNA gyrase subunit B (EC 5.99.1.3) | protein | 376 | 36% helix, 27% strand | I6WX66 |
| L | DNA gyrase subunit B (EC 5.99.1.3) | protein | 382 | 37% helix, 26% strand | I6WX66 |
| M | DNA gyrase subunit B (EC 5.99.1.3) | protein | 383 | 35% helix, 26% strand | I6WX66 |
| N | DNA gyrase subunit B (EC 5.99.1.3) | protein | 373 | 36% helix, 26% strand | I6WX66 |
| O | DNA gyrase subunit B (EC 5.99.1.3) | protein | 379 | 35% helix, 25% strand | I6WX66 |
| P | DNA gyrase subunit B (EC 5.99.1.3) | protein | 376 | 37% helix, 26% strand | I6WX66 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- MG · Magnesium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 168 | 0.83 | 0.98 | 36 | ANP, MG |
| 2 | 174 | 0.83 | 0.98 | 34 | ANP |
| 3 | 160 | 0.82 | 0.98 | 34 | ANP, MG |
| 4 | 163 | 0.82 | 0.98 | 34 | ANP |
| 5 | 172 | 0.82 | 0.97 | 41 | ANP, MG |
Interfaces
32 interfaces between chains.
- E–F · 2709 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2709 Ų buried · 43 hydrogen bonds · protein-protein
- M–N · 2613 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2564 Ų buried · 34 hydrogen bonds · protein-protein
- O–P · 2543 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3ZKB · 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 3ZKB · PDBe 3ZKB · UniProt I6WX66
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