MolNFT v1 · #41266 · protein
X-ray structure of oxalyl-CoA decarboxylase in complex with 3-deaza-thdp
2JI9: “X-ray structure of oxalyl-CoA decarboxylase in complex with 3-deaza-thdp”. X-ray diffraction, 3 ligands (TPW, ADP, MG), 4 pockets (best druggability 0.83). MolNFT v1 #41266 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2JI9
- Type
- protein
- Length
- 1,094 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
- TPW, ADP, MG
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxalyl-CoA decarboxylase (EC 4.1.1.8) | protein | 547 | 44% helix, 18% strand | P40149 |
Ligands and binding sites
- TPW · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-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
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.83 | 0.84 | 107 | TPW, MG, ADP |
| 2 | 928 | 0.82 | 0.83 | 115 | TPW, MG, ADP |
| 3 | 283 | 0.59 | 0.79 | 31 | empty |
| 4 | 304 | 0.59 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 3133 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2JI9 · X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP · 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 2JI9 · PDBe 2JI9 · UniProt P40149
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.