Research workbench

Ubij-SCP2 ubiquinone synthesis protein

Analyse Ubij-SCP2 ubiquinone synthesis protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H6P
Type: protein
Length: 463 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquinone biosynthesis protein ubij
UniProt: P0ADP7
Ligands: CA
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquinone biosynthesis protein ubij	protein	115	44% helix, 23% strand	P0ADP7
B	Ubiquinone biosynthesis protein ubij	protein	114	44% helix, 23% strand	P0ADP7
C	Ubiquinone biosynthesis protein ubij	protein	117	42% helix, 21% strand	P0ADP7
D	Ubiquinone biosynthesis protein ubij	protein	117	43% helix, 22% strand	P0ADP7

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, C, B, D
1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1003	0.83	0.84	89	CA
2	320	0.65	0.80	30	empty
3	339	0.64	0.78	33	empty
4	246	0.63	0.81	29	empty
5	276	0.63	0.80	29	empty

Interfaces

6 interfaces between chains.

B–D · 627 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 445 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 363 Å² buried · 1 hydrogen bond · protein-protein
A–B · 341 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 147 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6H6P · UbiJ-SCP2 Ubiqui synthesis protein · the same entry in another collection · chain D against D, TM-score 1.00
P0ADP7 · AlphaFold monomer V2.0 prediction for ubiquinone biosynthesis accessory factor ubij… · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P0ADP7
Elsewhere: RCSB PDB 6H6P · PDBe 6H6P · UniProt P0ADP7

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