MolNFT v1 · #51348 · protein
The structure of E. COLI ump kinase in complex with its allosteric regulator GTP
2V4Y · Uridylate kinase: “The structure of E. COLI ump kinase in complex with its allosteric regulator GTP”. X-ray diffraction, 1 ligand (GTP), 18 pockets (best druggability 0.85). MolNFT v1 #51348 on GenesisL1: 3D structure, binding sites…
- 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
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