Research workbench

Quadruple mutant of oxalyl-CoA decarboxylase from methylorubrum extorquens with bound tpp and ADP

Analyse Quadruple mutant of oxalyl-CoA decarboxylase from methylorubrum extorquens with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B2E
Type: protein
Length: 4,384 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 0.87

Structure

x-ray diffraction · 1 distinct chain · 45% 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	548	45% helix, 18% strand	C5AX46

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 8 copies · chains A, B, C, D, E, H, F, G
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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	708	0.87	0.91	97	ADP
2	537	0.84	0.90	61	empty
3	349	0.83	0.93	61	ADP
4	828	0.83	0.85	100	TPP, ADP, MG
5	456	0.83	0.90	59	empty

Interfaces

14 interfaces between chains.

C–D · 3384 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 3356 Å² buried · 45 hydrogen bonds · protein-protein
F–G · 3349 Å² buried · 42 hydrogen bonds · protein-protein
E–H · 3338 Å² buried · 43 hydrogen bonds · protein-protein
A–F · 1532 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7B2E · quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP… · 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 7B2E · PDBe 7B2E · UniProt C5AX46

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.