MolNFT v1 · #53211 · protein
Human orotate phosphoribosyltransferase (oprtase) domain of uridine 5'-monophosphate synthase (umps) in complex with its substrate orotidine 5'-monophosphate (omp)
2WNS: “Human orotate phosphoribosyltransferase (oprtase) domain of uridine 5'-monophosphate synthase (umps) in…”. X-ray diffraction, 2 ligands (OMP, CL), 4 pockets (best druggability 0.73). MolNFT v1 #53211 on GenesisL1: 3D structure…
- PDB
- 2WNS
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- P11172
- Ligands
- OMP, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 197 | 42% helix, 24% strand | P11172 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 199 | 43% helix, 24% strand | P11172 |
Ligands and binding sites
- OMP · Orotidine-5'-monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.73 | 0.99 | 22 | CL |
| 2 | 445 | 0.71 | 0.82 | 48 | OMP |
| 3 | 303 | 0.69 | 0.84 | 36 | OMP |
| 4 | 57 | 0.24 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1374 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2WNS · Human Orotate phosphoribosyltransferase (OPRTase) domain of Uridine 5' -monophosphate… · 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 B against A, TM-score 0.96
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 2WNS · PDBe 2WNS · UniProt P11172
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