Research workbench
1.80 ångström resolution crystal structure of orotidine 5'-phosphate decarboxylase from vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (ump)
Analyse 1.80 ångström resolution crystal structure of orotidine 5'-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UWQ
- Type
- protein
- Length
- 446 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
- Q9KQT7
- Ligands
- U5P
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 222 | 49% helix, 18% strand | Q9KQT7 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 224 | 50% helix, 17% strand | Q9KQT7 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.77 | 0.99 | 25 | empty |
| 2 | 418 | 0.69 | 0.81 | 50 | U5P, PEG, PGE |
| 3 | 412 | 0.67 | 0.80 | 46 | U5P |
Interfaces
1 interface between chains.
- A–B · 1771 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3UWQ · 1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQT7 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q9KQT7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9KQT7
- Elsewhere: RCSB PDB 3UWQ · PDBe 3UWQ · UniProt Q9KQT7
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