Research workbench
Human ump synthase (C-terminal domain-orotidine 5'-monophosphate decarboxylase)
Analyse Human ump synthase (C-terminal domain-orotidine 5'-monophosphate decarboxylase) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P1F
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase
- UniProt
- P11172
- Ligands
- NA, SO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine 5'-monophosphate synthase | protein | 259 | 44% helix, 17% strand | P11172 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.56 | 0.79 | 37 | SO4, NA, GOL |
| 2 | 59 | 0.50 | 0.86 | 16 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 2P1F · Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase) · 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 2P1F · PDBe 2P1F · UniProt P11172
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