SMTL ID : 5ojg.1

Crystal structure of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 30 residues within 4Å: Chain A: A.17, A.18, T.19, K.20, G.21, I.22, S.41, R.42, N.43, N.46, G.67, H.68, I.69, N.95, H.96, G.97, N.146, A.147, S.148, Y.161, K.165, P.191, G.192, V.193, I.194, T.196, K.197, M.198, S.199 Ligands: BUO.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.191 Hydrogen bonds: A:T.19, A:K.20, A:I.22, A:S.41, A:S.41, A:R.42, A:N.43, A:N.46, A:I.69, A:N.95, A:N.146, A:K.165, A:I.194, A:T.196, A:K.197, A:M.198, A:S.199, A:S.199 Water bridges: A:G.23, A:R.42, A:N.43, A:N.46, A:A.70, A:N.95 Salt bridges: A:R.42 NAP.3: 29 residues within 4Å: Chain B: A.17, T.19, K.20, G.21, I.22, S.41, R.42, N.43, N.46, G.67, H.68, I.69, N.95, H.96, G.97, N.146, A.147, S.148, Y.161, K.165, P.191, G.192, V.193, I.194, T.196, K.197, M.198, S.199 Ligands: BUO.4 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:P.191 Hydrogen bonds: B:T.19, B:T.19, B:K.20, B:I.22, B:S.41, B:S.41, B:R.42, B:N.43, B:N.46, B:I.69, B:N.95, B:N.146, B:Y.161, B:K.165, B:I.194, B:K.197, B:M.198, B:S.199, B:S.199 Water bridges: B:K.20, B:G.23, B:R.42, B:R.42, B:R.42, B:N.43, B:A.70, B:N.95, B:K.197, B:K.197, B:K.197 Salt bridges: B:K.20, B:R.42, B:K.197 NAP.5: 30 residues within 4Å: Chain C: A.17, A.18, T.19, K.20, G.21, I.22, S.41, R.42, N.43, N.46, G.67, H.68, I.69, N.95, H.96, G.97, N.146, A.147, S.148, Y.161, K.165, P.191, G.192, V.193, I.194, T.196, K.197, M.198, S.199 Ligands: BUO.6 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.191 Hydrogen bonds: C:T.19, C:K.20, C:I.22, C:S.41, C:S.41, C:R.42, C:N.43, C:N.46, C:I.69, C:N.95, C:N.146, C:K.165, C:I.194, C:T.196, C:K.197, C:M.198, C:S.199, C:S.199 Water bridges: C:G.23, C:R.42, C:N.43, C:N.46, C:A.70, C:N.95 Salt bridges: C:R.42 NAP.7: 29 residues within 4Å: Chain D: A.17, T.19, K.20, G.21, I.22, S.41, R.42, N.43, N.46, G.67, H.68, I.69, N.95, H.96, G.97, N.146, A.147, S.148, Y.161, K.165, P.191, G.192, V.193, I.194, T.196, K.197, M.198, S.199 Ligands: BUO.8 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:P.191 Hydrogen bonds: D:T.19, D:T.19, D:K.20, D:I.22, D:S.41, D:S.41, D:R.42, D:N.43, D:N.46, D:I.69, D:N.95, D:N.146, D:Y.161, D:K.165, D:I.194, D:K.197, D:M.198, D:S.199, D:S.199 Water bridges: D:K.20, D:G.23, D:R.42, D:R.42, D:R.42, D:N.43, D:A.70, D:N.95, D:K.197, D:K.197, D:K.197 Salt bridges: D:K.20, D:R.42, D:K.197

4 x BUO: butane-2,3-dione(Non-covalent)

BUO.2: 6 residues within 4Å: Chain A: S.148, S.150, I.158, Y.161, M.198 Ligands: NAP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.158, A:Y.161 Hydrogen bonds: A:S.148, A:S.150, A:Y.161 BUO.4: 6 residues within 4Å: Chain B: S.148, Y.149, S.150, Y.161, L.202 Ligands: NAP.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.149, B:Y.161 Hydrogen bonds: B:S.148 BUO.6: 6 residues within 4Å: Chain C: S.148, S.150, I.158, Y.161, M.198 Ligands: NAP.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.158, C:Y.161 Hydrogen bonds: C:S.148, C:S.150, C:Y.161 BUO.8: 6 residues within 4Å: Chain D: S.148, Y.149, S.150, Y.161, L.202 Ligands: NAP.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.149, D:Y.161 Hydrogen bonds: D:S.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kisiela, M. et al., Crystal structure and catalytic characterization of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans. FEBS J. (2018)

Release Date

2017-11-22

Peptides

Dehydrogenase/reductase SDR family member 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dehydrogenase/reductase SDR family member 4

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