MolNFT v1 · #49055 · protein
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to 5-iodo-ump
2QCH · Uridine 5'-monophosphate synthase (ump synthase): “Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase bound to…”. X-ray diffraction, 3 ligands (5IU, UMP, IOD), 4 pockets (best druggability…
- PDB
- 2QCH
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- 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
- 5IU, UMP, IOD
- Pockets
- 4 · 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 (ump synthase) (EC 4.1.1.23) | protein | 255 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- 5IU · 5-iodo-2'-deoxyuridine-5'-monophosphate · ligand · 2 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.76 | 0.94 | 32 | IOD, 5IU, UMP |
| 2 | 144 | 0.72 | 0.91 | 33 | IOD, 5IU, UMP |
| 3 | 50 | 0.31 | 0.77 | 16 | empty |
| 4 | 56 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1952 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2QCH · Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP… · 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 2QCH · PDBe 2QCH · UniProt P11172
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