MolNFT v1 · #32865 · protein
Crystal structure of oxalyl-CoA decarboxylase in complex with the cofactor derivative thiamin-2-thiazolone diphosphate and adenosine diphosphate
2C31: “Crystal structure of oxalyl-CoA decarboxylase in complex with the cofactor derivative thiamin-2-thiazolone…”. X-ray diffraction, 3 ligands (TZD, ADP, MG), 5 pockets (best druggability 0.82). MolNFT v1 #32865 on GenesisL1: 3D…
- PDB
- 2C31
- Type
- protein
- Length
- 1,092 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxalyl-CoA decarboxylase
- EC
- 4.1.1.8
- UniProt
- P40149
- Ligands
- TZD, ADP, MG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxalyl-CoA decarboxylase (EC 4.1.1.8) | protein | 546 | 46% helix, 18% strand | P40149 |
Ligands and binding sites
- TZD · 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-2-oxo-2,3-dihydro-1,3-thiazol-5-yl}ethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.82 | 0.83 | 113 | TZD, ADP |
| 2 | 908 | 0.82 | 0.83 | 102 | MG, TZD, ADP |
| 3 | 349 | 0.61 | 0.78 | 31 | empty |
| 4 | 328 | 0.61 | 0.78 | 33 | empty |
| 5 | 70 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3099 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2C31 · Crystal structure of oxalyl-CoA decarboxylase in complex with the cofactor derivative… · the same entry in another collection · chain A against A, TM-score 1.00
- P40149 · AlphaFold monomer V2.0 prediction for oxalyl-CoA decarboxylase (P40149) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P40149
- Elsewhere: RCSB PDB 2C31 · PDBe 2C31 · UniProt P40149
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