Research workbench
Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (C2 form)
Analyse Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (C2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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