MolNFT v1 · #63021 · protein
D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-ump, covalent adduct
3EWW · Orotidine-5'-phosphate decarboxylase: “D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-cyano-ump, covalent adduct”. X-ray diffraction, 1 ligand (U1P), 5 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3EWW
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine-5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- U1P
- Pockets
- 5 · 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 | Orotidine-5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 257 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- U1P · 6-[(E)-iminomethyl]uridine 5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 110 | 0.76 | 0.96 | 25 | U1P |
| 2 | 115 | 0.75 | 0.95 | 28 | U1P |
| 3 | 58 | 0.33 | 0.77 | 16 | empty |
| 4 | 52 | 0.31 | 0.77 | 13 | GOL |
| 5 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1919 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3EWW · D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with… · the same entry in another collection · chain B against B, 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 3EWW · PDBe 3EWW · UniProt P11172
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