MolNFT v1 · #118456 · protein

Thermostable aldehyde dehydrogenase from pyrobaculum sp. 1860 crystallized in microgravity (complex with NADP+)

5F2C: “Thermostable aldehyde dehydrogenase from pyrobaculum sp. 1860 crystallized in microgravity (complex with…”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.90). MolNFT v1 #118456 on GenesisL1: 3D structure…

PDB: 5F2C
Type: protein
Length: 3,887 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 0.90

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Aldehyde dehydrogenase	protein	487	41% helix, 22% strand	G7VCG0
B, E, G	Aldehyde dehydrogenase	protein	484	42% helix, 22% strand	G7VCG0
C, F	Aldehyde dehydrogenase	protein	489	42% helix, 22% strand	G7VCG0
D	Aldehyde dehydrogenase	protein	483	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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.90	0.93	136	empty
2	747	0.89	0.93	96	empty
3	680	0.87	0.91	77	empty
4	716	0.87	0.90	77	empty
5	575	0.86	0.92	78	empty

Interfaces

13 interfaces between chains.

E–F · 3624 Å² buried · 55 hydrogen bonds · protein-protein
A–B · 3581 Å² buried · 58 hydrogen bonds · protein-protein
G–H · 3571 Å² buried · 52 hydrogen bonds · protein-protein
C–D · 3526 Å² buried · 56 hydrogen bonds · protein-protein
E–H · 1218 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5F2C · Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 crystallized in… · 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 5F2C · PDBe 5F2C · UniProt G7VCG0

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