MolNFT v1 · #41268 · protein
X-ray structure of oxalyl-CoA decarboxylase in complex with coenzyme-a
2JIB: “X-ray structure of oxalyl-CoA decarboxylase in complex with coenzyme-a”. X-ray diffraction, 4 ligands (TPP, ADP, COA), 6 pockets (best druggability 0.86). MolNFT v1 #41268 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2JIB
- Type
- protein
- Length
- 1,118 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
- TPP, ADP, COA, MG
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxalyl-CoA decarboxylase (EC 4.1.1.8) | protein | 559 | 45% helix, 18% strand | P40149 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.86 | 0.87 | 115 | TPP, MG, ADP, COA, PGE |
| 2 | 1077 | 0.85 | 0.86 | 122 | TPP, MG, ADP, COA, PGE |
| 3 | 313 | 0.61 | 0.79 | 31 | empty |
| 4 | 303 | 0.59 | 0.78 | 33 | empty |
| 5 | 138 | 0.48 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3875 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 2JIB · X-ray structure of Oxalyl-CoA decarboxylase in complex with coenzyme- A · 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 2JIB · PDBe 2JIB · UniProt P40149
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.