Research workbench
The structure of E. COLI ump kinase in complex with UTP
Analyse The structure of E. COLI ump kinase in complex with UTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BNF
- Type
- protein
- Length
- 472 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.4
- UniProt
- P29464
- Ligands
- UTP
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.4) | protein | 236 | 39% helix, 19% strand | P29464 |
| B | Uridylate kinase (EC 2.7.4.4) | protein | 236 | 39% helix, 19% strand | P29464 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.64 | 0.79 | 52 | UTP |
| 2 | 279 | 0.59 | 0.79 | 45 | UTP |
| 3 | 92 | 0.38 | 0.76 | 23 | GOL |
| 4 | 91 | 0.37 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1282 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 2BNF · The structure of E. coli UMP kinase in complex with UTP · the same entry in another collection · chain A against A, 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 P29464
- Elsewhere: RCSB PDB 2BNF · PDBe 2BNF · UniProt P29464
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