SMTL ID : 3l77.1

X-ray structure alcohol dehydrogenase from archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

NJP.1: 31 residues within 4Å: Chain A: G.9, A.10, S.11, R.12, G.13, I.14, A.33, R.34, S.35, L.59, D.60, V.61, S.62, N.87, A.88, G.89, V.110, T.136, T.137, S.138, D.139, Y.151, K.155, P.179, G.180, A.181, V.182, T.184, Y.185, F.186 Ligands: GOL.7 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:F.186 Hydrogen bonds: A:S.11, A:S.11, A:S.11, A:R.12, A:I.14, A:R.34, A:S.35, A:D.60, A:D.60, A:V.61, A:S.62, A:G.89, A:D.139, A:D.139, A:Y.151, A:Y.151, A:K.155, A:K.155, A:V.182, A:V.182, A:T.184, A:T.184, A:T.184, A:Y.185, A:F.186 Salt bridges: A:R.12, A:R.34 pi-Cation interactions: A:R.34 Water bridges: A:R.12, A:G.15, A:R.34, A:R.34, A:S.62, A:S.62, A:N.87 NJP.13: 31 residues within 4Å: Chain B: G.9, A.10, S.11, R.12, G.13, I.14, A.33, R.34, S.35, L.59, D.60, V.61, S.62, N.87, A.88, G.89, V.110, T.136, T.137, S.138, D.139, Y.151, K.155, P.179, G.180, A.181, V.182, T.184, Y.185, F.186 Ligands: GOL.19 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:F.186 Hydrogen bonds: B:S.11, B:S.11, B:S.11, B:R.12, B:I.14, B:R.34, B:S.35, B:D.60, B:D.60, B:V.61, B:S.62, B:G.89, B:D.139, B:D.139, B:Y.151, B:Y.151, B:K.155, B:K.155, B:V.182, B:V.182, B:T.184, B:T.184, B:T.184, B:Y.185, B:F.186 Salt bridges: B:R.12, B:R.34 pi-Cation interactions: B:R.34 Water bridges: B:R.12, B:G.15, B:R.34, B:R.34, B:S.62, B:S.62, B:N.87 NJP.25: 31 residues within 4Å: Chain C: G.9, A.10, S.11, R.12, G.13, I.14, A.33, R.34, S.35, L.59, D.60, V.61, S.62, N.87, A.88, G.89, V.110, T.136, T.137, S.138, D.139, Y.151, K.155, P.179, G.180, A.181, V.182, T.184, Y.185, F.186 Ligands: GOL.31 35 PLIP interactions: 35 interactions with chain C Hydrophobic interactions: C:F.186 Hydrogen bonds: C:S.11, C:S.11, C:S.11, C:R.12, C:I.14, C:R.34, C:S.35, C:D.60, C:V.61, C:S.62, C:G.89, C:D.139, C:D.139, C:D.139, C:Y.151, C:Y.151, C:K.155, C:K.155, C:V.182, C:V.182, C:T.184, C:T.184, C:Y.185, C:F.186 Salt bridges: C:R.12, C:R.34 pi-Cation interactions: C:R.34 Water bridges: C:R.12, C:G.15, C:R.34, C:R.34, C:S.62, C:S.62, C:N.87 NJP.37: 31 residues within 4Å: Chain D: G.9, A.10, S.11, R.12, G.13, I.14, A.33, R.34, S.35, L.59, D.60, V.61, S.62, N.87, A.88, G.89, V.110, T.136, T.137, S.138, D.139, Y.151, K.155, P.179, G.180, A.181, V.182, T.184, Y.185, F.186 Ligands: GOL.43 35 PLIP interactions: 35 interactions with chain D Hydrophobic interactions: D:F.186 Hydrogen bonds: D:S.11, D:S.11, D:S.11, D:R.12, D:I.14, D:R.34, D:S.35, D:D.60, D:V.61, D:S.62, D:G.89, D:D.139, D:D.139, D:D.139, D:Y.151, D:Y.151, D:K.155, D:K.155, D:V.182, D:V.182, D:T.184, D:T.184, D:Y.185, D:F.186 Salt bridges: D:R.12, D:R.34 pi-Cation interactions: D:R.34 Water bridges: D:R.12, D:G.15, D:R.34, D:R.34, D:S.62, D:S.62, D:N.87

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.170, D.171 Chain B: V.229 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: V.54, F.55, Y.56 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain A: F.93, S.138, D.139, V.140, R.143, I.145, G.180, A.181, Q.231 Ligands: NJP.1 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain A: D.124, R.128 Ligand excluded by PLIP GOL.9: 9 residues within 4Å: Chain A: K.3, Y.27, V.83, L.132, R.173, L.213, L.215, P.216, K.217 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: V.229 Chain B: P.170, D.171 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: V.54, F.55, Y.56 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain B: F.93, S.138, D.139, V.140, R.143, I.145, G.180, A.181, Q.231 Ligands: NJP.13 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain B: D.124, R.128 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain B: K.3, Y.27, V.83, L.132, R.173, L.213, L.215, P.216, K.217 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: P.170, D.171 Chain D: V.229 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain C: V.54, F.55, Y.56 Ligand excluded by PLIP GOL.31: 10 residues within 4Å: Chain C: F.93, S.138, D.139, V.140, R.143, I.145, G.180, A.181, Q.231 Ligands: NJP.25 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain C: D.124, R.128 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain C: K.3, Y.27, V.83, L.132, R.173, L.213, L.215, P.216, K.217 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain C: V.229 Chain D: P.170, D.171 Ligand excluded by PLIP GOL.40: 3 residues within 4Å: Chain D: V.54, F.55, Y.56 Ligand excluded by PLIP GOL.43: 10 residues within 4Å: Chain D: F.93, S.138, D.139, V.140, R.143, I.145, G.180, A.181, Q.231 Ligands: NJP.37 Ligand excluded by PLIP GOL.44: 2 residues within 4Å: Chain D: D.124, R.128 Ligand excluded by PLIP GOL.45: 9 residues within 4Å: Chain D: K.3, Y.27, V.83, L.132, R.173, L.213, L.215, P.216, K.217 Ligand excluded by PLIP

12 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain A: F.93, Y.147, F.186, G.187, Y.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.199 PG4.5: 5 residues within 4Å: Chain A: H.105, E.106, E.109 Chain C: H.105 Ligands: PG4.29 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.62, A:S.62, A:E.109, C:H.105 PG4.12: 13 residues within 4Å: Chain A: A.142, R.159, R.163, R.178, E.223 Chain B: A.142, R.159, R.163, R.178, E.223 Ligands: EDO.10, EDO.22, PG4.24 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.159, A:R.163, A:R.163, A:R.178, B:R.159, B:R.159, B:R.163 Water bridges: A:A.142, A:R.178, B:A.142, B:R.163, B:R.178 PG4.15: 5 residues within 4Å: Chain B: F.93, Y.147, F.186, G.187, Y.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.199 PG4.17: 5 residues within 4Å: Chain B: H.105, E.106, E.109 Chain D: H.105 Ligands: PG4.41 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.62, B:S.62, B:E.109, D:H.105 PG4.24: 13 residues within 4Å: Chain A: A.142, R.159, R.163, R.178, E.223 Chain B: A.142, R.159, R.163, R.178, E.223 Ligands: EDO.10, PG4.12, EDO.22 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.159, A:R.159, A:R.163, B:R.159, B:R.163, B:R.163, B:R.178 Water bridges: A:A.142, A:R.163, A:R.178, B:A.142, B:R.178 PG4.27: 5 residues within 4Å: Chain C: F.93, Y.147, F.186, G.187, Y.199 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.199, C:Y.199 PG4.29: 5 residues within 4Å: Chain A: H.105 Chain C: H.105, E.106, E.109 Ligands: PG4.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:H.105, C:S.62, C:S.62 Water bridges: C:E.106 PG4.36: 13 residues within 4Å: Chain C: A.142, R.159, R.163, R.178, E.223 Chain D: A.142, R.159, R.163, R.178, E.223 Ligands: EDO.34, EDO.46, PG4.48 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:R.159, C:R.163, C:R.163, C:R.178, D:R.159, D:R.159, D:R.163 Water bridges: C:A.142, C:R.178, D:A.142, D:R.163, D:R.178 PG4.39: 5 residues within 4Å: Chain D: F.93, Y.147, F.186, G.187, Y.199 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.199, D:Y.199 PG4.41: 5 residues within 4Å: Chain B: H.105 Chain D: H.105, E.106, E.109 Ligands: PG4.17 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:H.105, D:S.62, D:S.62 Water bridges: D:E.106 PG4.48: 13 residues within 4Å: Chain C: A.142, R.159, R.163, R.178, E.223 Chain D: A.142, R.159, R.163, R.178, E.223 Ligands: EDO.34, PG4.36, EDO.46 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:R.159, C:R.159, C:R.163, D:R.159, D:R.163, D:R.163, D:R.178 Water bridges: C:A.142, C:R.163, C:R.178, D:A.142, D:R.178

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

EDO.6: 6 residues within 4Å: Chain A: E.1, K.3, D.25, G.26, Y.27, K.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.3, A:G.26, A:K.214, A:K.214 Water bridges: A:K.3 EDO.10: 7 residues within 4Å: Chain A: A.142, R.159, R.163 Chain C: W.156 Ligands: PG4.12, PG4.24, EDO.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.159 Water bridges: A:R.159, A:R.163 EDO.11: 3 residues within 4Å: Chain A: R.12, R.38, Y.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.12, A:R.12, A:Y.185 Water bridges: A:R.38 EDO.18: 6 residues within 4Å: Chain B: E.1, K.3, D.25, G.26, Y.27, K.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.3, B:G.26, B:K.214, B:K.214 Water bridges: B:K.3 EDO.22: 7 residues within 4Å: Chain B: A.142, R.159, R.163 Chain D: W.156 Ligands: PG4.12, PG4.24, EDO.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.159 Water bridges: B:R.159, B:R.163 EDO.23: 3 residues within 4Å: Chain B: R.12, R.38, Y.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.12, B:R.12, B:Y.185 Water bridges: B:R.38 EDO.30: 6 residues within 4Å: Chain C: E.1, K.3, D.25, G.26, Y.27, K.214 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.3, C:G.26, C:K.214, C:K.214 Water bridges: C:K.3 EDO.34: 7 residues within 4Å: Chain A: W.156 Chain C: A.142, R.159, R.163 Ligands: EDO.10, PG4.36, PG4.48 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.159 Water bridges: C:R.159, C:R.163 EDO.35: 3 residues within 4Å: Chain C: R.12, R.38, Y.185 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.12, C:R.12 Water bridges: C:R.38 EDO.42: 6 residues within 4Å: Chain D: E.1, K.3, D.25, G.26, Y.27, K.214 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.3, D:G.26, D:K.214, D:K.214 Water bridges: D:K.3 EDO.46: 7 residues within 4Å: Chain B: W.156 Chain D: A.142, R.159, R.163 Ligands: EDO.22, PG4.36, PG4.48 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.159 Water bridges: D:R.159, D:R.163 EDO.47: 3 residues within 4Å: Chain D: R.12, R.38, Y.185 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.12, D:R.12 Water bridges: D:R.38

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Lyashenko, A.V. et al., X-ray structure alcohol dehydrogenase from archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP. To be Published

Release Date

2011-01-19

Peptides

Short-chain alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Short-chain alcohol dehydrogenase