SMTL ID : 3tn7.1

Crystal structure of short-chain alcohol dehydrogenase from hyperthermophilic archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

4 x NJP: 5-hydroxy-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NJP.1: 30 residues within 4Å: Chain A: G.31, A.32, S.33, R.34, G.35, I.36, A.55, R.56, S.57, L.81, D.82, V.83, S.84, N.109, A.110, G.111, V.132, T.158, T.159, S.160, D.161, Y.173, K.177, P.201, G.202, A.203, V.204, T.206, Y.207, F.208 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.208 Hydrogen bonds: A:S.33, A:S.33, A:S.33, A:R.34, A:I.36, A:R.56, A:S.57, A:D.82, A:D.82, A:V.83, A:S.84, A:G.111, A:D.161, A:D.161, A:Y.173, A:Y.173, A:K.177, A:K.177, A:V.204, A:V.204, A:T.206, A:T.206, A:Y.207, A:F.208 Water bridges: A:R.34, A:R.34, A:G.37, A:S.84, A:S.84, A:N.109 Salt bridges: A:R.34, A:R.56 NJP.3: 30 residues within 4Å: Chain B: G.31, A.32, S.33, R.34, G.35, I.36, A.55, R.56, S.57, L.81, D.82, V.83, S.84, N.109, A.110, G.111, V.132, T.158, T.159, S.160, D.161, Y.173, K.177, P.201, G.202, A.203, V.204, T.206, Y.207, F.208 34 PLIP interactions: 34 interactions with chain B Hydrogen bonds: B:S.33, B:S.33, B:S.33, B:R.34, B:I.36, B:R.56, B:S.57, B:D.82, B:V.83, B:S.84, B:A.110, B:G.111, B:D.161, B:D.161, B:D.161, B:Y.173, B:Y.173, B:K.177, B:V.204, B:V.204, B:T.206, B:T.206, B:T.206, B:Y.207, B:F.208 Water bridges: B:R.34, B:R.34, B:G.37, B:S.84, B:S.84, B:N.109 Salt bridges: B:R.34, B:R.56 pi-Stacking: B:F.208 NJP.4: 30 residues within 4Å: Chain C: G.31, A.32, S.33, R.34, G.35, I.36, A.55, R.56, S.57, L.81, D.82, V.83, S.84, N.109, A.110, G.111, V.132, T.158, T.159, S.160, D.161, Y.173, K.177, P.201, G.202, A.203, V.204, T.206, Y.207, F.208 34 PLIP interactions: 34 interactions with chain C Hydrophobic interactions: C:F.208 Hydrogen bonds: C:S.33, C:S.33, C:S.33, C:R.34, C:I.36, C:R.56, C:S.57, C:D.82, C:V.83, C:S.84, C:G.111, C:D.161, C:D.161, C:D.161, C:Y.173, C:Y.173, C:K.177, C:K.177, C:V.204, C:V.204, C:T.206, C:T.206, C:T.206, C:Y.207, C:F.208 Water bridges: C:R.34, C:R.34, C:G.37, C:S.84, C:S.84, C:N.109 Salt bridges: C:R.34, C:R.56 NJP.6: 30 residues within 4Å: Chain D: G.31, A.32, S.33, R.34, G.35, I.36, A.55, R.56, S.57, L.81, D.82, V.83, S.84, N.109, A.110, G.111, V.132, T.158, T.159, S.160, D.161, Y.173, K.177, P.201, G.202, A.203, V.204, T.206, Y.207, F.208 33 PLIP interactions: 33 interactions with chain D Hydrogen bonds: D:S.33, D:S.33, D:S.33, D:R.34, D:I.36, D:R.56, D:S.57, D:D.82, D:D.82, D:V.83, D:S.84, D:A.110, D:G.111, D:D.161, D:D.161, D:Y.173, D:Y.173, D:K.177, D:V.204, D:V.204, D:T.206, D:T.206, D:Y.207, D:F.208 Water bridges: D:R.34, D:R.34, D:G.37, D:S.84, D:S.84, D:N.109 Salt bridges: D:R.34, D:R.56 pi-Stacking: D:F.208

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: K.25, Y.49, V.105, L.154, R.195, L.235, L.237, P.238, K.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.49, A:R.195, A:R.195 Water bridges: A:L.234 GOL.5: 9 residues within 4Å: Chain C: K.25, Y.49, V.105, L.154, R.195, L.235, L.237, P.238, K.239 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.195, C:R.195 Water bridges: C:L.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezsudnova, E.Y. et al., Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus. Biochimie (2012)

Release Date

2012-08-15

Peptides

Short-chain alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Short-chain alcohol dehydrogenase