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Crystal structure of an acyl-CoA dehydrogenase domain protein from burkholderia phymatum bound to FAD

Analyse Crystal structure of an acyl-CoA dehydrogenase domain protein from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IDU
Type: protein
Length: 1,578 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-CoA dehydrogenase domain protein
UniProt: B2JPK4
Ligands: FAD
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 58% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Acyl-CoA dehydrogenase domain protein	protein	392	59% helix, 16% strand	B2JPK4
B	Acyl-CoA dehydrogenase domain protein	protein	389	58% helix, 16% strand	B2JPK4
C	Acyl-CoA dehydrogenase domain protein	protein	405	58% helix, 16% strand	B2JPK4

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
EDO · 1,2-ethanediol · additive · 11 copies · chains A, D, B, C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.86	0.91	67	FAD, EDO
2	573	0.85	0.90	82	FAD
3	798	0.85	0.88	104	FAD, EDO
4	887	0.85	0.86	90	FAD, EDO
5	451	0.62	0.76	38	EDO

Interfaces

6 interfaces between chains.

B–C · 2152 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1965 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1700 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1686 Å² buried · 38 hydrogen bonds · protein-protein
B–D · 240 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5IDU · Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum… · 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 B2JPK4
Elsewhere: RCSB PDB 5IDU · PDBe 5IDU · UniProt B2JPK4

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