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Crystal structure of yeast COQ5 in the apo form

Analyse Crystal structure of yeast COQ5 in the apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OBX
Type: protein
Length: 940 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
EC: 2.1.1.201
UniProt: P49017
Ligands: TAM
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C, B	2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (EC 2.1.1.201)	protein	235	49% helix, 22% strand	P49017

Ligands and binding sites

TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A, D, C, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.74	0.77	89	empty
2	629	0.69	0.77	75	empty
3	255	0.66	0.83	39	empty
4	239	0.66	0.83	36	empty
5	68	0.48	0.83	20	empty

Interfaces

6 interfaces between chains.

A–B · 1057 Å² buried · 0 hydrogen bonds · protein-protein
D–C · 1051 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 261 Å² buried · 3 hydrogen bonds · protein-protein
C–B · 258 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 41 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4OBX · Crystal structure of yeast Coq5 in the apo form · the same entry in another collection · chain B against B, TM-score 1.00
P49017 · AlphaFold monomer V2.0 prediction for 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase… · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P49017
Elsewhere: RCSB PDB 4OBX · PDBe 4OBX · UniProt P49017

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