SMTL ID : 5u0l.1

X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from Marinobacter aquaeolei VT8 complexed with a substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: Q.264, G.398, F.399, D.400, R.427 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.399, A:D.400, A:D.400, A:R.427 EDO.2: 8 residues within 4Å: Chain A: F.152, G.153, K.179, P.180, S.181, E.182, F.229 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.153, A:K.179, A:E.182 EDO.3: 6 residues within 4Å: Chain A: A.446, S.447, S.448, A.449 Chain B: V.134, A.135 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.135, A:S.448 Water bridges: A:S.448 EDO.4: 4 residues within 4Å: Chain A: H.129, R.142, R.144 Chain B: V.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.129, A:R.144, A:R.144 EDO.5: 8 residues within 4Å: Chain A: N.258, R.293, L.381, E.382, D.383, T.392, Y.394, N.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.258, A:D.383, A:T.392, A:N.408 EDO.6: 9 residues within 4Å: Chain A: R.126, H.461, P.463, Y.467, D.470 Chain B: D.470, A.473, W.474, P.475 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.473, A:D.470 Water bridges: A:R.126 EDO.8: 7 residues within 4Å: Chain A: F.152, K.179, S.212, G.215, K.216, V.235 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.212 EDO.9: 8 residues within 4Å: Chain A: F.157, L.161, R.287, C.288, T.289, T.444, F.452 Ligands: 8YP.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.287, A:C.288, A:T.289

1 x 8YP: decanal(Non-covalent)

8YP.7: 13 residues within 4Å: Chain A: K.115, H.160, L.161, G.164, H.165, T.230, E.254, A.446, S.448, F.452, S.464, A.465 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161, A:E.254, A:A.465

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 4 residues within 4Å: Chain B: Q.264, G.398, F.399, R.427 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.427, B:R.427 MPD.11: 8 residues within 4Å: Chain A: H.240, L.251, N.460, R.462 Chain B: I.250, L.251, N.460, R.462 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.251, B:L.251 Hydrogen bonds: A:H.240, A:N.460, B:L.251, B:N.460, B:R.462

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 1 residues within 4Å: Chain B: R.144 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 4 residues within 4Å: Chain A: R.422 Chain B: E.131, H.138, E.480 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.422, B:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertram, J.H. et al., Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket. Appl. Environ. Microbiol. (2017)

Release Date

2017-04-26

Peptides

N-succinylglutamate 5-semialdehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-succinylglutamate 5-semialdehyde dehydrogenase

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