SMTL ID : 9feb.1

Short-chain dehydrogenase/reductase (SDR) from Thermus caliditerrae in complex with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-pentamer

Ligands

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

NAP.1: 24 residues within 4Å: Chain A: G.36, A.37, S.38, R.39, G.40, G.42, V.59, A.60, R.61, K.62, G.84, D.85, V.86, A.87, N.112, A.113, G.114, F.115, V.116, L.117, T.118, R.131, V.135, L.214 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.116 Hydrogen bonds: A:G.36, A:G.36, A:S.38, A:S.38, A:R.39, A:R.61, A:R.61, A:K.62, A:D.85, A:D.85, A:V.86, A:V.116 Water bridges: A:R.39, A:R.39, A:G.114, A:G.114, A:T.118, A:T.118 Salt bridges: A:R.39, A:R.39, A:R.61, A:K.62 pi-Cation interactions: A:R.61 NAP.3: 33 residues within 4Å: Chain B: G.36, A.37, S.38, R.39, G.40, I.41, G.42, V.59, A.60, R.61, K.62, G.84, D.85, V.86, A.87, N.112, A.113, G.114, F.115, V.135, N.136, I.162, S.163, S.164, T.165, Y.177, K.181, P.207, G.208, F.209, T.210, T.212, L.214 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:P.207 Hydrogen bonds: B:G.36, B:G.36, B:S.38, B:S.38, B:R.39, B:I.41, B:R.61, B:K.62, B:D.85, B:D.85, B:V.86, B:I.162, B:K.181, B:T.210 Water bridges: B:R.39, B:R.39, B:R.39, B:R.39, B:R.39, B:R.39, B:G.40, B:G.42, B:N.112, B:G.114, B:F.115, B:Y.177, B:T.210, B:T.212, B:T.212, B:T.212 Salt bridges: B:R.39, B:R.61 pi-Cation interactions: B:R.61 NAP.5: 33 residues within 4Å: Chain C: G.36, A.37, S.38, R.39, G.40, I.41, G.42, V.59, A.60, R.61, K.62, G.84, D.85, V.86, A.87, N.112, A.113, G.114, V.135, I.162, S.163, S.164, T.165, Y.177, K.181, P.207, G.208, F.209, T.210, T.212, D.213, L.214, L.215 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:P.207 Hydrogen bonds: C:G.36, C:G.36, C:S.38, C:S.38, C:R.39, C:I.41, C:R.61, C:K.62, C:D.85, C:V.86, C:I.162, C:Y.177, C:K.181, C:T.210, C:T.210, C:T.212, C:T.212, C:D.213, C:L.214 Water bridges: C:R.39, C:R.39, C:R.39, C:R.39, C:G.42, C:N.112, C:D.213 Salt bridges: C:R.39, C:R.39, C:R.61 NAP.6: 33 residues within 4Å: Chain D: G.36, A.37, S.38, R.39, G.40, I.41, G.42, V.59, A.60, R.61, K.62, G.84, D.85, V.86, A.87, N.112, A.113, G.114, V.135, I.162, S.163, S.164, T.165, Y.177, K.181, P.207, G.208, F.209, T.210, T.212, D.213, L.214, L.215 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:G.36, D:G.36, D:S.38, D:S.38, D:R.39, D:I.41, D:R.61, D:K.62, D:D.85, D:V.86, D:I.162, D:Y.177, D:K.181, D:T.210, D:T.210, D:D.213, D:L.214 Water bridges: D:N.112, D:G.114 Salt bridges: D:R.39, D:R.61

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 1 residues within 4Å: Chain C: G.282 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sosa, Y. et al., In silico enzyme screening identifies an SDR ketoreductase from Thermus caliditerrae as an attractive biocatalyst and promising candidate for protein engineering. Front Chem Biol (2024)

Release Date

2024-06-26

Peptides

SDR family oxidoreductase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

SDR family oxidoreductase

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