MolNFT v1 · #32337 · protein
The structure of E.COLI ump kinase in complex with udp
2BND · Uridylate kinase: “The structure of E.COLI ump kinase in complex with udp”. X-ray diffraction, 2 ligands (UDP, POP), 5 pockets (best druggability 0.62). MolNFT v1 #32337 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BND
- Type
- protein
- Length
- 474 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
- UDP, POP
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.4) | protein | 237 | 38% helix, 18% strand | P29464 |
| B | Uridylate kinase (EC 2.7.4.4) | protein | 237 | 39% helix, 19% strand | P29464 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.62 | 0.81 | 41 | UDP |
| 2 | 151 | 0.58 | 0.83 | 31 | UDP |
| 3 | 179 | 0.50 | 0.77 | 23 | empty |
| 4 | 80 | 0.39 | 0.78 | 24 | GOL |
| 5 | 91 | 0.37 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2BND · The structure of E. coli UMP kinase in complex with UDP · 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 2BND · PDBe 2BND · UniProt P29464
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