SMTL ID : 9b2f.1

Crystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

NAD.1: 28 residues within 4Å: Chain A: G.36, C.37, D.38, T.39, G.40, F.41, L.61, L.82, D.83, V.84, T.85, N.112, A.113, G.114, V.115, V.136, V.162, S.163, S.164, Y.176, K.180, P.206, G.207, L.208, F.209, T.211, E.212, L.213 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.41, A:P.206 Hydrogen bonds: A:D.38, A:T.39, A:T.39, A:T.39, A:T.39, A:F.41, A:D.83, A:V.84, A:N.112, A:G.114, A:K.180, A:F.209, A:F.209, A:T.211, A:E.212 Water bridges: A:G.36, A:G.42, A:N.112, A:L.213 NAD.3: 28 residues within 4Å: Chain B: G.36, C.37, D.38, T.39, G.40, F.41, L.61, L.82, D.83, V.84, T.85, N.112, A.113, G.114, V.115, V.136, V.162, S.163, S.164, Y.176, K.180, P.206, G.207, L.208, F.209, T.211, E.212, L.213 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:F.41, B:P.206 Hydrogen bonds: B:D.38, B:D.38, B:T.39, B:T.39, B:T.39, B:T.39, B:F.41, B:D.83, B:D.83, B:V.84, B:N.112, B:G.114, B:Y.176, B:K.180, B:F.209, B:F.209, B:E.212 Water bridges: B:G.36, B:G.42, B:N.112, B:L.213

2 x MLI: MALONATE ION

MLI.2: 3 residues within 4Å: Chain A: H.296 Chain B: H.296 Ligands: MLI.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.296, B:H.296, A:H.296 MLI.4: 3 residues within 4Å: Chain A: H.296 Chain B: H.296 Ligands: MLI.2 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.296, A:H.296, A:H.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pakhomova, S. et al., The large substrate binding pocket of dehydrogenase reductase 9 underlies its ability to oxidize diverse pro-inflammatory and pro-resolving oxylipins. To Be Published

Release Date

2025-03-19

Peptides

Dehydrogenase/reductase SDR family member 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dehydrogenase/reductase SDR family member 9

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