MolNFT v1 · #62590 · protein

Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308

3EK1: “Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.88). MolNFT v1 #62590 on GenesisL1: 3D structure, binding sites and…

PDB: 3EK1
Type: protein
Length: 3,865 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase
EC: 1.2.1.16
UniProt: Q2YRI3
Ligands: SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aldehyde dehydrogenase (EC 1.2.1.16)	protein	485	41% helix, 23% strand	Q2YRI3
B, C, D, E, F, H	Aldehyde dehydrogenase (EC 1.2.1.16)	protein	483	42% helix, 24% strand	Q2YRI3
G	Aldehyde dehydrogenase (EC 1.2.1.16)	protein	482	43% helix, 24% strand	Q2YRI3

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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	1053	0.88	0.89	120	empty
2	1085	0.88	0.89	126	empty
3	1085	0.88	0.89	126	empty
4	1182	0.88	0.89	74	empty
5	1065	0.86	0.87	106	empty

Interfaces

14 interfaces between chains.

A–D · 2577 Å² buried · 41 hydrogen bonds · protein-protein
F–G · 2512 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 2507 Å² buried · 38 hydrogen bonds · protein-protein
E–H · 2506 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 1063 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

3EK1 · Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308 · 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 Q2YRI3
Elsewhere: RCSB PDB 3EK1 · PDBe 3EK1 · UniProt Q2YRI3

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