SMTL ID : 4zz7.1 (2 other biounits)

Crystal structure of methylmalonate-semialdehyde dehydrogenase (DddC) from Oceanimonas doudoroffii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

3 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: I.148, T.149, P.150, F.151, N.152, W.160, K.175, P.176, S.177, E.178, R.179, G.206, K.208, V.211, F.225, V.226, G.227, S.228, I.231, L.249, G.250, G.251, C.283, E.385, F.387, N.413, F.452 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.226 Hydrogen bonds: A:T.149, A:T.149, A:F.151, A:K.175, A:S.177, A:E.178, A:K.208, A:K.208, A:S.228, A:G.250, A:E.385, A:N.413 Water bridges: A:R.179 Salt bridges: A:R.179 NAD.2: 27 residues within 4Å: Chain C: I.148, T.149, P.150, F.151, N.152, W.160, K.175, P.176, S.177, E.178, R.179, K.208, V.211, F.225, V.226, G.227, S.228, I.231, Y.234, L.249, G.250, G.251, C.283, E.385, F.387, N.413, F.452 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.226 Hydrogen bonds: C:T.149, C:F.151, C:K.175, C:E.178, C:S.228, C:G.250, C:E.385, C:N.413 Salt bridges: C:R.179 NAD.3: 25 residues within 4Å: Chain D: I.148, T.149, P.150, F.151, N.152, W.160, K.175, S.177, E.178, R.179, K.208, V.211, F.225, V.226, G.227, S.228, I.231, L.249, G.250, G.251, C.283, E.385, F.387, N.413, F.452 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:P.150, D:V.226 Hydrogen bonds: D:T.149, D:F.151, D:K.175, D:E.178, D:S.228, D:S.228, D:A.252, D:E.385, D:N.413 Water bridges: D:N.413 Salt bridges: D:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Do, H. et al., Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii. J. Microbiol. (2016)

Release Date

2016-04-06

Peptides

Methylmalonate-semialdehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methylmalonate-semialdehyde dehydrogenase

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