Research workbench
Ump kinase from pyrococcus furiosus complexed with its substrate ump and its substrate analog amppnp
Analyse Ump kinase from pyrococcus furiosus complexed with its substrate ump and its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BMU
- Type
- protein
- Length
- 451 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.-
- UniProt
- Q8U122
- Ligands
- ANP, U5P, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.-) | protein | 225 | 46% helix, 16% strand | Q8U122 |
| B | Uridylate kinase (EC 2.7.4.-) | protein | 226 | 47% helix, 14% strand | Q8U122 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.74 | 0.85 | 55 | MG, ANP, U5P |
| 2 | 366 | 0.73 | 0.85 | 54 | ANP, U5P, MG |
| 3 | 170 | 0.47 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2BMU · Ump kinase from pyrococcus furiosus complexed with its substrate ump and its substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8U122 · AlphaFold monomer V2.0 prediction for uridylate kinase (Q8U122) · a predicted model of the same protein · chain A 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 Q8U122
- Elsewhere: RCSB PDB 2BMU · PDBe 2BMU · UniProt Q8U122
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