SMTL ID : 6y4d.1

Crystal structure of a short-chain dehydrogenase/reductase (SDR) from Zephyranthes treatiae in complex with NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: G.52, T.54, K.55, I.57, S.76, R.77, N.78, E.81, C.101, D.102, I.103, N.130, A.131, G.132, V.153, V.180, S.181, S.182, Y.195, K.199, P.225, G.226, A.227, I.228, T.230, S.232, S.233 Ligands: GOL.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:T.54, A:K.55, A:I.57, A:R.77, A:N.78, A:E.81, A:D.102, A:D.102, A:I.103, A:N.130, A:G.132, A:G.132, A:Y.195, A:K.199, A:I.228, A:I.228, A:T.230, A:S.232 Water bridges: A:S.76, A:R.77, A:N.130, A:N.130, A:G.133, A:S.232, A:S.232 Salt bridges: A:K.55, A:R.77 NAP.4: 27 residues within 4Å: Chain B: G.52, T.54, K.55, I.57, S.76, R.77, N.78, E.81, C.101, D.102, I.103, N.130, A.131, G.132, V.153, V.180, S.181, S.182, Y.195, K.199, P.225, G.226, A.227, I.228, T.230, S.232 Ligands: GOL.5 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:T.54, B:K.55, B:I.57, B:R.77, B:N.78, B:E.81, B:D.102, B:I.103, B:A.104, B:N.130, B:G.132, B:G.132, B:K.199, B:I.228, B:I.228, B:T.230, B:T.230, B:S.232 Water bridges: B:G.58, B:S.76, B:N.130, B:S.232, B:S.232 Salt bridges: B:K.55, B:R.77 NAP.6: 28 residues within 4Å: Chain C: G.52, T.54, K.55, I.57, S.76, R.77, N.78, E.81, C.101, D.102, I.103, N.130, A.131, G.132, V.153, V.180, S.181, S.182, Y.195, K.199, P.225, G.226, A.227, I.228, T.230, S.232, S.233 Ligands: GOL.7 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:T.54, C:K.55, C:I.57, C:R.77, C:N.78, C:E.81, C:D.102, C:D.102, C:I.103, C:N.130, C:G.132, C:G.132, C:Y.195, C:K.199, C:I.228, C:I.228, C:T.230, C:S.232 Water bridges: C:S.76, C:R.77, C:N.130, C:N.130, C:G.133, C:S.232, C:S.232 Salt bridges: C:K.55, C:R.77 NAP.9: 27 residues within 4Å: Chain D: G.52, T.54, K.55, I.57, S.76, R.77, N.78, E.81, C.101, D.102, I.103, N.130, A.131, G.132, V.153, V.180, S.181, S.182, Y.195, K.199, P.225, G.226, A.227, I.228, T.230, S.232 Ligands: GOL.10 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:T.54, D:K.55, D:I.57, D:R.77, D:N.78, D:E.81, D:D.102, D:I.103, D:A.104, D:N.130, D:G.132, D:G.132, D:K.199, D:I.228, D:I.228, D:T.230, D:T.230, D:S.232 Water bridges: D:G.58, D:S.76, D:N.130, D:S.232, D:S.232 Salt bridges: D:K.55, D:R.77

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.134, H.192, F.236, E.246 Ligands: NAP.1 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: R.254, E.257, E.259, E.260 Chain B: S.274 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.259, A:E.259 Water bridges: B:S.274 GOL.5: 3 residues within 4Å: Chain B: Y.134, F.236 Ligands: NAP.4 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain C: Y.134, H.192, F.236, E.246 Ligands: NAP.6 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain C: R.254, E.257, E.259, E.260 Chain D: S.274 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.259, C:E.259 Water bridges: D:S.274 GOL.10: 3 residues within 4Å: Chain D: Y.134, F.236 Ligands: NAP.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roth, S. et al., Crossing the Border: From Keto- to Imine Reduction in Short-Chain Dehydrogenases/Reductases. Chembiochem (2020)

Release Date

2020-04-29

Peptides

short-chain dehydrogenase/reductase (SDR): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

short-chain dehydrogenase/reductase (SDR)