SMTL ID : 8bb8.1

Crystal structure of human aldehyde dehydrogenase ALDH3A1 in complex with octanal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 2 residues within 4Å: Chain A: T.335, D.336 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.336, H2O.4, H2O.10 K.2: 3 residues within 4Å: Chain A: K.453, Y.456, P.458 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain B: E.93, W.94, A.96 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.93, B:A.96 K.7: 2 residues within 4Å: Chain B: K.453, Y.456 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.453, B:Y.456, H2O.26, H2O.27

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: N.448, D.449, K.453, Y.456 Chain B: V.240, R.243, R.244 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.453, A:Y.456 Hydrogen bonds: A:D.449, A:D.449 Salt bridges: B:R.243, B:R.244 ACT.8: 7 residues within 4Å: Chain A: R.243, R.244 Chain B: M.447, N.448, D.449, K.453, Y.456 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.243, A:R.244 Hydrophobic interactions: B:K.453, B:Y.456 Hydrogen bonds: B:D.449, B:Y.456, B:Y.456

2 x OYA: OCTANAL(Non-covalent)

OYA.4: 11 residues within 4Å: Chain A: Y.79, N.128, Y.129, N.132, L.133, Q.136, C.257, I.408, T.409, H.427 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.79, A:Y.79, A:Y.129, A:T.409 Hydrogen bonds: A:N.128 Water bridges: A:C.257 OYA.9: 10 residues within 4Å: Chain B: Y.79, Y.129, N.132, L.133, Q.136, T.256, C.257, I.408, T.409, H.427 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.79, B:Y.79, B:L.133, B:T.409 Hydrogen bonds: B:C.257

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: Y.79, E.82, E.83, Q.136, T.409, H.411, H.427, G.428 Ligands: OYA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.82, A:E.82, A:E.83, A:Q.136, A:T.409, A:G.428 Water bridges: A:H.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boichot, V. et al., Characterization of human oxidoreductases involved in aldehyde odorant metabolism. Sci Rep (2023)

Release Date

2023-04-19

Peptides

Aldehyde dehydrogenase, dimeric NADP-preferring: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde dehydrogenase, dimeric NADP-preferring