Research workbench
Ump kinase from pyrococcus furiosus complexed with its substrate analog amppnp
Analyse Ump kinase from pyrococcus furiosus complexed with its substrate analog amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BRI
- Type
- protein
- Length
- 450 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, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate kinase (EC 2.7.4.-) | protein | 225 | 47% helix, 16% strand | Q8U122 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.70 | 0.80 | 51 | ANP, MG |
| 2 | 453 | 0.65 | 0.78 | 48 | ANP, MG |
| 3 | 97 | 0.55 | 0.85 | 23 | empty |
| 4 | 188 | 0.47 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1321 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2BRI · Ump kinase from pyrococcus furiosus complexed with its substrate analog amppnp · 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 2BRI · PDBe 2BRI · UniProt Q8U122
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