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Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 6-iodo-ump
Analyse Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BGJ
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- U5P
- Pockets
- 6 · best druggability 0.73
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 (EC 4.1.1.23) | protein | 257 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.73 | 0.97 | 25 | U5P |
| 2 | 92 | 0.71 | 0.94 | 31 | U5P |
| 3 | 50 | 0.37 | 0.81 | 14 | empty |
| 4 | 53 | 0.35 | 0.79 | 14 | empty |
| 5 | 53 | 0.32 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1941 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3BGJ · Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified… · 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 3BGJ · PDBe 3BGJ · UniProt P11172
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