Research workbench
The structure of E. COLI ump kinase in complex with its allosteric regulator GTP
Analyse The structure of E. COLI ump kinase in complex with its allosteric regulator GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V4Y
- Type
- protein
- Length
- 1,407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P0A7E9
- Ligands
- GTP
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uridylate kinase (EC 2.7.4.22) | protein | 237 | 39% helix, 18% strand | P0A7E9 |
| B | Uridylate kinase (EC 2.7.4.22) | protein | 231 | 39% helix, 19% strand | P0A7E9 |
| D | Uridylate kinase (EC 2.7.4.22) | protein | 233 | 39% helix, 18% strand | P0A7E9 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 236 | 39% helix, 19% strand | P0A7E9 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 233 | 39% helix, 19% strand | P0A7E9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 12 copies · chains A, E, F, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.85 | 0.87 | 133 | GTP |
| 2 | 167 | 0.80 | 0.96 | 37 | empty |
| 3 | 154 | 0.78 | 0.95 | 35 | empty |
| 4 | 399 | 0.62 | 0.77 | 62 | GTP |
| 5 | 175 | 0.61 | 0.83 | 32 | empty |
Interfaces
12 interfaces between chains.
- C–E · 1346 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1321 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 1313 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 936 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 935 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2V4Y · The structure of E. COLI ump kinase in complex with its allosteric regulator GTP · the same entry in another collection · chain F against F, TM-score 1.00
- P0A7E9 · AlphaFold monomer V2.0 prediction for uridylate kinase (P0A7E9) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 P0A7E9
- Elsewhere: RCSB PDB 2V4Y · PDBe 2V4Y · UniProt P0A7E9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.