Research workbench
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 6-NH2-ump
Analyse Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DBP
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- NUP, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 257 | 44% helix, 17% strand | P11172 |
Ligands and binding sites
- NUP · 6-aminouridine 5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.77 | 0.96 | 31 | NUP |
| 2 | 103 | 0.75 | 0.96 | 29 | NUP |
| 3 | 52 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1960 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3DBP · Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Complexed with… · 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 3DBP · PDBe 3DBP · UniProt P11172
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