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Thermostable aldehyde dehydrogenase from pyrobaculum SP.1860 complexed with NADP+

Analyse Thermostable aldehyde dehydrogenase from pyrobaculum SP.1860 complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EKC
Type: protein
Length: 3,877 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase
UniProt: G7VCG0
Ligands: NAP
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 7 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Aldehyde dehydrogenase	protein	484	43% helix, 23% strand	G7VCG0
B	Aldehyde dehydrogenase	protein	485	42% helix, 23% strand	G7VCG0
C	Aldehyde dehydrogenase	protein	483	42% helix, 22% strand	G7VCG0
D	Aldehyde dehydrogenase	protein	484	43% helix, 22% strand	G7VCG0
E	Aldehyde dehydrogenase	protein	490	43% helix, 22% strand	G7VCG0
F	Aldehyde dehydrogenase	protein	482	43% helix, 23% strand	G7VCG0
H	Aldehyde dehydrogenase	protein	485	42% helix, 23% strand	G7VCG0

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

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	1114	0.91	0.93	135	empty
2	1135	0.90	0.93	135	empty
3	639	0.87	0.91	85	empty
4	613	0.86	0.91	77	empty
5	603	0.86	0.91	74	empty

Interfaces

14 interfaces between chains.

G–H · 3606 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 3589 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 3550 Å² buried · 56 hydrogen bonds · protein-protein
E–F · 3527 Å² buried · 52 hydrogen bonds · protein-protein
F–G · 1204 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5EKC · Thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 complexed with NADP+ · 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 G7VCG0
Elsewhere: RCSB PDB 5EKC · PDBe 5EKC · UniProt G7VCG0

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