MolNFT v1 · #118287 · protein

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

5EXF: “Thermostable aldehyde dehydrogenase from pyrobaculum SP.1860 complexed with NADP+”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.89). MolNFT v1 #118287 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5EXF
Type: protein
Length: 3,885 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 0.89

Structure

x-ray diffraction · 7 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aldehyde dehydrogenase	protein	488	42% helix, 22% strand	G7VCG0
B, E	Aldehyde dehydrogenase	protein	483	41% helix, 22% strand	G7VCG0
C	Aldehyde dehydrogenase	protein	489	42% helix, 22% strand	G7VCG0
D	Aldehyde dehydrogenase	protein	483	43% helix, 23% strand	G7VCG0
F	Aldehyde dehydrogenase	protein	488	43% helix, 22% strand	G7VCG0
G	Aldehyde dehydrogenase	protein	484	42% helix, 23% strand	G7VCG0
H	Aldehyde dehydrogenase	protein	487	42% helix, 22% strand	G7VCG0

Ligands and binding sites

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

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	713	0.89	0.93	89	empty
2	587	0.87	0.93	81	empty
3	654	0.86	0.90	77	empty
4	561	0.86	0.91	77	empty
5	682	0.86	0.90	79	empty

Interfaces

13 interfaces between chains.

A–B · 3604 Å² buried · 53 hydrogen bonds · protein-protein
C–D · 3575 Å² buried · 50 hydrogen bonds · protein-protein
E–F · 3570 Å² buried · 49 hydrogen bonds · protein-protein
G–H · 3521 Å² buried · 50 hydrogen bonds · protein-protein
F–G · 1216 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5EXF · 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 5EXF · PDBe 5EXF · UniProt G7VCG0

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