MolNFT v1 · #80696 · protein

Crystal structure of NAD-dependent aldehyde dehydrogenase from sinorhizobium meliloti

3U4J: “Crystal structure of NAD-dependent aldehyde dehydrogenase from sinorhizobium meliloti”. X-ray diffraction, 1 ligand (CA), 13 pockets (best druggability 0.88). MolNFT v1 #80696 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3U4J
Type: protein
Length: 2,015 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent aldehyde dehydrogenase
UniProt: Q930S8
Ligands: CA
Pockets: 13 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	NAD-dependent aldehyde dehydrogenase	protein	505	40% helix, 22% strand	Q930S8
B	NAD-dependent aldehyde dehydrogenase	protein	502	39% helix, 23% strand	Q930S8
D	NAD-dependent aldehyde dehydrogenase	protein	503	40% helix, 23% strand	Q930S8

Ligands and binding sites

CA · Calcium ion · metal · chains A

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

Pockets

13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.88	0.93	110	empty
2	322	0.84	0.94	36	empty
3	900	0.77	0.80	103	empty
4	841	0.77	0.80	105	empty
5	395	0.76	0.86	56	empty

Interfaces

6 interfaces between chains.

C–D · 3387 Å² buried · 50 hydrogen bonds · protein-protein
A–B · 3347 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 1283 Å² buried · 37 hydrogen bonds · protein-protein
B–D · 1273 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 1107 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

3U4J · Crystal structure of NAD-dependent aldehyde dehydrogenase from Sinorhizobium meliloti · 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 Q930S8
Elsewhere: RCSB PDB 3U4J · PDBe 3U4J · UniProt Q930S8

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