Research workbench
Crystal structure of umpk from M. tuberculosis in complex with udp and UTP (P21212 form)
Analyse Crystal structure of umpk from M. tuberculosis in complex with udp and UTP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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