Research workbench
UMP/CMP kinase from slime mold complexed with ADP, udp, beryllium fluoride
Analyse UMP/CMP kinase from slime mold complexed with ADP, udp, beryllium fluoride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UKD
- Type
- protein
- Length
- 191 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE kinase
- EC
- 2.7.4.14
- UniProt
- P20425
- Ligands
- ADP, UDP, BF2, MG
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE kinase (EC 2.7.4.14) | protein | 191 | 55% helix, 15% strand | P20425 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- UDP · Uridine-5'-diphosphate · ligand · chains A
- BF2 · Beryllium difluoride · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.73 | 0.86 | 43 | MG, ADP, UDP, BF2 |
Compared structures
- 4UKD · UMP/CMP kinase from slime mold complexed with ADP, udp, beryllium fluoride · the same entry in another collection · chain A against A, TM-score 1.00
- P20425 · AlphaFold monomer V2.0 prediction for ump-cmp kinase (P20425) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P20425
- Elsewhere: RCSB PDB 4UKD · PDBe 4UKD · UniProt P20425
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