MolNFT v1 · #161299 · protein
R80A mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis
6QA2: “R80A mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (TAM, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #161299 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6QA2
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- A5U5E1
- Ligands
- TAM, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 135 | 45% helix, 19% strand | A5U5E1 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 124 | 35% helix, 19% strand | A5U5E1 |
| D, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 123 | 35% helix, 24% strand | A5U5E1 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 128 | 41% helix, 20% strand | A5U5E1 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains B, D, F, A, C, E
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.82 | 0.83 | 70 | TAM |
| 2 | 160 | 0.44 | 0.75 | 25 | SO4 |
| 3 | 136 | 0.43 | 0.76 | 27 | SO4 |
| 4 | 67 | 0.28 | 0.73 | 15 | SO4 |
Interfaces
10 interfaces between chains.
- C–D · 683 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 677 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 670 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 551 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 551 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6QA2 · R80A mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis · the same entry in another collection · chain F against F, TM-score 1.00
- A5U5E1 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (A5U5E1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A5U5E1
- Elsewhere: RCSB PDB 6QA2 · PDBe 6QA2 · UniProt A5U5E1
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