SMTL ID : 5ilg.1

Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: G.102, I.103, M.199 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.102 MG.7: 4 residues within 4Å: Chain B: G.26, T.197, D.198 Ligands: NAD.8 No protein-ligand interaction detected (PLIP)

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

NAD.2: 33 residues within 4Å: Chain A: G.22, A.24, G.25, G.26, I.27, D.47, L.48, Q.49, M.72, D.73, V.74, V.100, A.101, G.102, I.103, R.111, V.115, M.145, S.146, S.147, Y.160, K.164, P.192, G.193, A.194, T.195, T.197, D.198, M.199, F.200 Ligands: MG.1, IPH.3, EDO.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.192 Hydrogen bonds: A:G.22, A:I.27, A:L.48, A:D.73, A:V.74, A:A.101, A:Y.160, A:K.164, A:T.195, A:T.195, A:T.197, A:M.199 Water bridges: A:G.26, A:G.26, A:G.26, A:G.28, A:R.111, A:D.198, A:D.198, A:D.198 NAD.8: 30 residues within 4Å: Chain B: G.22, G.25, G.26, I.27, D.47, L.48, Q.49, M.72, D.73, V.74, V.100, A.101, G.102, I.103, R.111, V.115, M.145, S.146, Y.160, K.164, P.192, G.193, A.194, T.195, T.197, D.198, M.199, F.200 Ligands: MG.7, IPH.9 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.192 Hydrogen bonds: B:I.27, B:L.48, B:Q.49, B:D.73, B:V.74, B:A.101, B:G.102, B:K.164, B:T.195, B:T.195, B:T.195, B:T.197, B:T.197, B:D.198, B:M.199 Water bridges: B:G.26, B:G.28, B:R.111, B:D.198

2 x IPH: PHENOL(Non-covalent)

IPH.3: 10 residues within 4Å: Chain A: S.147, V.149, I.157, Y.160, P.192, A.194, F.200, I.219 Ligands: NAD.2, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.149, A:I.157, A:Y.160, A:F.200, A:I.219 Hydrogen bonds: A:S.147, A:Y.160 IPH.9: 9 residues within 4Å: Chain B: S.147, I.157, Y.160, P.192, G.193, A.194, F.200, I.219 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.157, B:Y.160, B:F.200, B:I.219 Hydrogen bonds: B:S.147, B:S.147, B:Y.160

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

EDO.4: 4 residues within 4Å: Chain A: G.193, A.194, R.222 Ligands: IPH.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.194 Water bridges: A:D.152 EDO.5: 5 residues within 4Å: Chain A: R.14, G.15, G.39, A.41, Q.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.15 EDO.6: 5 residues within 4Å: Chain A: A.24, G.25, D.47, Q.49 Ligands: NAD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.47 Water bridges: A:G.26, A:Q.49, A:D.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofmann, L. et al., Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family. Biochemistry (2016)

Release Date

2016-11-16

Peptides

Photoreceptor dehydrogenase, isoform C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Photoreceptor dehydrogenase, isoform C

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