MolNFT v1 · #173401 · protein
Oxalyl-CoA decarboxylase from methylorubrum extorquens with bound tpp and ADP
7AYG · Putative oxalyl-CoA decarboxylase (oxc, yfdu): “Oxalyl-CoA decarboxylase from methylorubrum extorquens with bound tpp and ADP”. X-ray diffraction, 3 ligands (TPP, ADP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #173401 on…
- PDB
- 7AYG
- Type
- protein
- Length
- 4,368 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxalyl-CoA decarboxylase (oxc, yfdu)
- EC
- 4.1.1.8
- UniProt
- C5AX46
- Ligands
- TPP, ADP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative oxalyl-CoA decarboxylase (oxc, yfdu) (EC 4.1.1.8) | protein | 546 | 46% helix, 18% strand | C5AX46 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.89 | 0.92 | 119 | ADP |
| 2 | 871 | 0.88 | 0.91 | 123 | TPP, ADP, MG |
| 3 | 707 | 0.87 | 0.91 | 90 | ADP |
| 4 | 589 | 0.87 | 0.92 | 97 | ADP |
| 5 | 891 | 0.81 | 0.83 | 101 | TPP, ADP, MG |
Interfaces
14 interfaces between chains.
- A–B · 3341 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 3319 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3298 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 3293 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1571 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7AYG · oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP · the same entry in another collection · 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 C5AX46
- Elsewhere: RCSB PDB 7AYG · PDBe 7AYG · UniProt C5AX46
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.