Research workbench

Crystals structure of acyl-CoA oxidase-1 in caenorhabditis elegans, apo form-II

Analyse Crystals structure of acyl-CoA oxidase-1 in caenorhabditis elegans, apo form-II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K3H
Type: protein
Length: 5,072 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-coenzyme a oxidase
UniProt: O62140
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-coenzyme a oxidase	protein	634	58% helix, 10% strand	O62140
B, E	Acyl-coenzyme a oxidase	protein	635	58% helix, 10% strand	O62140
C	Acyl-coenzyme a oxidase	protein	633	58% helix, 10% strand	O62140
D, G, H	Acyl-coenzyme a oxidase	protein	634	57% helix, 10% strand	O62140
F	Acyl-coenzyme a oxidase	protein	633	57% helix, 10% strand	O62140

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	1008	0.86	0.87	95	empty
2	542	0.85	0.90	55	empty
3	538	0.84	0.90	55	empty
4	546	0.84	0.90	53	empty
5	625	0.84	0.89	79	empty

Interfaces

9 interfaces between chains.

G–H · 5813 Å² buried · 72 hydrogen bonds · protein-protein
E–F · 5770 Å² buried · 70 hydrogen bonds · protein-protein
A–B · 5728 Å² buried · 71 hydrogen bonds · protein-protein
C–D · 5718 Å² buried · 74 hydrogen bonds · protein-protein
B–C · 529 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5K3H · Crystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans, Apo form-II · the same entry in another collection · chain H against H, TM-score 1.00
O62140 · AlphaFold monomer V2.0 prediction for acyl-coenzyme a oxidase acox-1.1 (O62140) · a predicted model of the same protein · chain D 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 O62140
Elsewhere: RCSB PDB 5K3H · PDBe 5K3H · UniProt O62140

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