MolNFT v1 · #32338 · protein
The structure of E. COLI ump kinase in complex with ump
2BNE · Uridylate kinase: “The structure of E. COLI ump kinase in complex with ump”. X-ray diffraction, 1 ligand (U5P), 4 pockets (best druggability 0.62). MolNFT v1 #32338 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BNE
- 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
- U5P
- Pockets
- 4 · best druggability 0.62
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 | 234 | 39% helix, 19% strand | P29464 |
| B | Uridylate kinase (EC 2.7.4.4) | protein | 238 | 38% helix, 18% strand | P29464 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · 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 | 281 | 0.62 | 0.80 | 42 | U5P |
| 2 | 232 | 0.60 | 0.80 | 42 | U5P |
| 3 | 105 | 0.41 | 0.76 | 25 | empty |
| 4 | 65 | 0.35 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1246 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2BNE · The structure of E. coli UMP kinase in complex with UMP · the same entry in another collection · chain B against B, 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 2BNE · PDBe 2BNE · UniProt P29464
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