MolNFT v1 · #49060 · protein
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (ASP312ASN mutant) of human ump synthase bound to 6- hydroxymethyl-ump
2QCM · Uridine 5'-monophosphate synthase (ump synthase): “Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (ASP312ASN mutant) of human ump…”. X-ray diffraction, 1 ligand (JW5), 1 pocket (best druggability 0.54).…
- PDB
- 2QCM
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase (ump synthase)
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- JW5
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine 5'-monophosphate synthase (ump synthase) (EC 4.1.1.23) | protein | 257 | 44% helix, 17% strand | P11172 |
Ligands and binding sites
- JW5 · 6-(hydroxymethyl)uridine 5'-(dihydrogen phosphate) · ligand · 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 | 208 | 0.54 | 0.78 | 30 | JW5 |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 2QCM · Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn… · 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 2QCM · PDBe 2QCM · UniProt P11172
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