MolNFT v1 · #123292 · protein

Crystal structure of rhodopseudomonas palustris propionaldehyde dehydrogenase with bound NAD+

5JFL: “Crystal structure of rhodopseudomonas palustris propionaldehyde dehydrogenase with bound NAD+”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.79). MolNFT v1 #123292 on GenesisL1: 3D structure, binding sites and…

PDB: 5JFL
Type: protein
Length: 3,526 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase
UniProt: Q21A49
Ligands: NAD
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Aldehyde dehydrogenase	protein	440	44% helix, 21% strand	Q21A49
B, C, E, H	Aldehyde dehydrogenase	protein	439	44% helix, 20% strand	Q21A49
D, G	Aldehyde dehydrogenase	protein	445	44% helix, 21% strand	Q21A49

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · 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	486	0.79	0.87	62	empty
2	372	0.79	0.89	44	empty
3	706	0.79	0.83	64	empty
4	1095	0.79	0.81	124	empty
5	780	0.71	0.77	54	empty

Interfaces

15 interfaces between chains.

B–D · 2490 Å² buried · 54 hydrogen bonds · protein-protein
F–H · 2456 Å² buried · 53 hydrogen bonds · protein-protein
A–C · 2430 Å² buried · 52 hydrogen bonds · protein-protein
E–G · 2386 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 1297 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5JFL · Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound… · 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 Q21A49
Elsewhere: RCSB PDB 5JFL · PDBe 5JFL · UniProt Q21A49

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