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Crystal structure of an acyl-acp dehydrogenase

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

PDB: 4XVX
Type: protein
Length: 744 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-[acyl-carrier-protein] dehydrogenase mbtn
EC: 1.3.99.-
UniProt: P9WQF9
Ligands: FDA
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-[acyl-carrier-protein] dehydrogenase mbtn (EC 1.3.99.-)	protein	371	59% helix, 16% strand	P9WQF9
B	Acyl-[acyl-carrier-protein] dehydrogenase mbtn (EC 1.3.99.-)	protein	373	58% helix, 16% strand	P9WQF9

Ligands and binding sites

FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
P6G · Hexaethylene glycol · additive · chains B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	763	0.86	0.89	82	P6G, FDA
2	751	0.86	0.89	78	P33, FDA
3	263	0.54	0.77	47	empty
4	149	0.46	0.77	14	empty
5	83	0.34	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 2093 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

4XVX · Crystal structure of an acyl-ACP dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
P9WQF9 · AlphaFold monomer V2.0 prediction for acyl-[acyl-carrier-protein] dehydrogenase mbtn… · a predicted model of the same protein · chain A 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 P9WQF9
Elsewhere: RCSB PDB 4XVX · PDBe 4XVX · UniProt P9WQF9

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