MolNFT v1 · #174039 · protein
Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (C2 form)
7BIX · Uridylate kinase: “Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (C2 form)”. X-ray diffraction, 2 ligands (UDP, UTP), 20 pockets (best druggability 0.78). MolNFT v1 #174039 on GenesisL1: 3D structure…
- PDB
- 7BIX
- Type
- protein
- Length
- 2,701 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P9WHK5
- Ligands
- UDP, UTP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 11 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 224 | 38% helix, 18% strand | P9WHK5 |
| B | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 42% helix, 18% strand | P9WHK5 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 229 | 40% helix, 19% strand | P9WHK5 |
| D, H | Uridylate kinase (EC 2.7.4.22) | protein | 225 | 40% helix, 18% strand | P9WHK5 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 224 | 40% helix, 17% strand | P9WHK5 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 220 | 42% helix, 18% strand | P9WHK5 |
| G | Uridylate kinase (EC 2.7.4.22) | protein | 219 | 39% helix, 17% strand | P9WHK5 |
| I | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 41% helix, 17% strand | P9WHK5 |
| J | Uridylate kinase (EC 2.7.4.22) | protein | 228 | 40% helix, 18% strand | P9WHK5 |
| K | Uridylate kinase (EC 2.7.4.22) | protein | 228 | 39% helix, 19% strand | P9WHK5 |
| L | Uridylate kinase (EC 2.7.4.22) | protein | 227 | 40% helix, 19% strand | P9WHK5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains B, C, D, E, H, I, J, K
- UTP · Uridine 5'-triphosphate · ligand · 6 copies · chains A, C, E, B, D, G, I, K, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.78 | 0.87 | 56 | empty |
| 2 | 645 | 0.78 | 0.83 | 68 | UTP |
| 3 | 366 | 0.77 | 0.87 | 60 | empty |
| 4 | 637 | 0.76 | 0.82 | 68 | UTP |
| 5 | 842 | 0.75 | 0.79 | 110 | UDP |
Interfaces
19 interfaces between chains.
- C–D · 1422 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1419 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1366 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1364 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1352 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7BIX · Crystal structure of UMPK from M. tuberculosis in complex with UDP and UTP (C2 form) · the same entry in another collection · chain L against L, 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 P9WHK5
- Elsewhere: RCSB PDB 7BIX · PDBe 7BIX · UniProt P9WHK5
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