MolNFT v1 · #58986 · protein
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-cn-ump
3BK0 · Uridine 5'-monophosphate synthase: “Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-cn-ump”. X-ray diffraction, 2 ligands (CNU, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #58986 on…
- PDB
- 3BK0
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- CNU, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine 5'-monophosphate synthase (EC 4.1.1.23) | protein | 257 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- CNU · 5-cyano-uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.76 | 0.95 | 31 | CNU |
| 2 | 133 | 0.74 | 0.93 | 33 | CNU |
| 3 | 69 | 0.34 | 0.76 | 16 | GOL |
| 4 | 52 | 0.33 | 0.78 | 15 | empty |
| 5 | 56 | 0.32 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1935 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3BK0 · Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P11172 · AlphaFold monomer V2.0 prediction for uridine 5'-monophosphate synthase (P11172) · a predicted model of the same protein · 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 P11172
- Elsewhere: RCSB PDB 3BK0 · PDBe 3BK0 · UniProt P11172
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