MolNFT v1 · #174106 · protein
Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (P21212 form)
7BL7 · Uridylate kinase: “Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (P21212 form)”. X-ray diffraction, 2 ligands (UDP, UTP), 20 pockets (best druggability 0.79). MolNFT v1 #174106 on GenesisL1: 3D…
- PDB
- 7BL7
- Type
- protein
- Length
- 2,574 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 0.79
Structure
x-ray diffraction · 11 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uridylate kinase (EC 2.7.4.22) | protein | 227 | 41% helix, 18% strand | P9WHK5 |
| A | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 41% helix, 19% strand | P9WHK5 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 216 | 42% helix, 19% strand | P9WHK5 |
| E, H | Uridylate kinase (EC 2.7.4.22) | protein | 222 | 44% helix, 18% strand | P9WHK5 |
| D | Uridylate kinase (EC 2.7.4.22) | protein | 228 | 40% helix, 18% strand | P9WHK5 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 230 | 40% helix, 20% strand | P9WHK5 |
| I | Uridylate kinase (EC 2.7.4.22) | protein | 225 | 40% helix, 19% strand | P9WHK5 |
| J | Uridylate kinase (EC 2.7.4.22) | protein | 227 | 39% helix, 19% strand | P9WHK5 |
| K | Uridylate kinase (EC 2.7.4.22) | protein | 224 | 42% helix, 18% strand | P9WHK5 |
| L | Uridylate kinase (EC 2.7.4.22) | protein | 158 | 41% helix, 21% strand | P9WHK5 |
| G | Uridylate kinase (EC 2.7.4.22) | protein | 169 | 40% helix, 20% strand | P9WHK5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains B, E, D, C, I, J, K, H
- UTP · Uridine 5'-triphosphate · ligand · 8 copies · chains A, C, F, D, K, B, E, I, J, L, H, G
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 | 697 | 0.79 | 0.84 | 77 | UTP |
| 2 | 299 | 0.78 | 0.89 | 53 | empty |
| 3 | 476 | 0.76 | 0.84 | 67 | UTP |
| 4 | 719 | 0.73 | 0.79 | 96 | UDP |
| 5 | 672 | 0.73 | 0.80 | 98 | UDP |
Interfaces
25 interfaces between chains.
- G–H · 1434 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 1430 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1408 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1390 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 1359 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7BL7 · Crystal structure of UMPK from M. tuberculosis in complex with UDP and UTP (P21212 form) · the same entry in another collection · chain H against H, 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 7BL7 · PDBe 7BL7 · UniProt P9WHK5
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