SMTL ID : 7utc.1

Crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus with NADP and transition-state analogue inhibitor DMSO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: C.37, S.39, H.59, E.60, D.150 Ligands: NAP.2, DMS.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:H.59, A:D.150 ZN.12: 7 residues within 4Å: Chain B: C.37, S.39, H.59, E.60, D.150 Ligands: NAP.13, DMS.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:H.59, B:D.150 ZN.22: 6 residues within 4Å: Chain C: C.37, S.39, H.59, D.150 Ligands: NAP.23, DMS.24 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.37, C:H.59, C:D.150 ZN.34: 6 residues within 4Å: Chain D: C.37, S.39, H.59, D.150 Ligands: NAP.35, DMS.38 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.37, D:H.59, D:D.150

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

NAP.2: 29 residues within 4Å: Chain A: C.37, T.38, S.39, H.42, D.150, T.154, G.174, I.175, G.176, P.177, V.178, V.197, S.199, R.200, I.223, A.242, G.243, G.244, I.248, V.265, N.266, Y.267, G.293, L.294, A.295, K.340 Chain B: M.285 Ligands: ZN.1, DMS.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.154 Hydrogen bonds: A:T.38, A:H.42, A:I.175, A:G.176, A:V.178, A:S.199, A:R.200, A:R.200, A:V.265, A:Y.267, A:A.295 Water bridges: A:G.179, A:N.245 Salt bridges: A:R.200, A:K.340 NAP.13: 28 residues within 4Å: Chain A: M.285 Chain B: C.37, T.38, S.39, H.42, D.150, T.154, G.174, I.175, G.176, P.177, V.178, S.199, R.200, I.223, A.242, G.243, G.244, I.248, V.265, N.266, Y.267, G.293, L.294, A.295, K.340 Ligands: ZN.12, DMS.15 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.154, B:V.178 Hydrogen bonds: B:T.38, B:I.175, B:G.176, B:V.178, B:S.199, B:S.199, B:R.200, B:R.200, B:Y.267, B:G.293, B:A.295 Water bridges: B:T.38, B:G.179, B:G.179 Salt bridges: B:R.200, B:R.200, B:K.340 NAP.23: 30 residues within 4Å: Chain C: C.37, T.38, S.39, H.42, D.150, T.154, G.174, I.175, G.176, P.177, V.178, V.197, S.199, R.200, Y.218, I.223, A.242, G.243, G.244, I.248, V.265, N.266, Y.267, G.293, L.294, A.295, K.340 Chain D: M.285 Ligands: ZN.22, DMS.24 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:T.154, C:V.178 Hydrogen bonds: C:T.38, C:H.42, C:I.175, C:G.176, C:G.176, C:V.178, C:S.199, C:R.200, C:V.265, C:Y.267, C:A.295 Water bridges: C:T.38, C:H.42, C:H.42, C:G.179, C:G.244, C:N.245, C:N.245, C:N.266 Salt bridges: C:R.200, C:R.200, C:K.340, C:K.340 pi-Stacking: C:Y.218, C:Y.218 NAP.35: 30 residues within 4Å: Chain C: M.285 Chain D: C.37, T.38, S.39, H.42, D.150, T.154, G.174, I.175, G.176, P.177, V.178, V.197, S.199, R.200, Y.218, I.223, A.242, G.243, G.244, I.248, V.265, N.266, Y.267, G.293, L.294, A.295, K.340 Ligands: ZN.34, DMS.38 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:T.154, D:V.178 Hydrogen bonds: D:T.38, D:I.175, D:G.176, D:G.176, D:V.178, D:S.199, D:S.199, D:R.200, D:R.200, D:V.265, D:Y.267, D:A.295 Water bridges: D:T.38, D:G.179, D:R.200 Salt bridges: D:R.200, D:K.340 pi-Stacking: D:Y.218, D:Y.218

35 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: F.25, R.91, D.128 Chain C: F.25, R.91 Ligands: DMS.27 Ligand excluded by PLIP DMS.4: 6 residues within 4Å: Chain A: V.95, G.98, Y.99, H.100 Chain C: V.95, Q.96 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain A: C.37, S.39, H.59, I.86, W.110, D.150 Ligands: ZN.1, NAP.2 Ligand excluded by PLIP DMS.6: 7 residues within 4Å: Chain A: L.300, R.304, D.307 Chain D: G.167, T.169, D.237, K.257 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: Y.209, Y.210, V.314, D.315 Ligand excluded by PLIP DMS.8: 9 residues within 4Å: Chain A: M.1, K.2, K.17, E.18, K.19, P.20, G.121, E.122, F.123 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: P.137, D.307, F.310, Y.311 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: P.296, R.301, R.304 Ligand excluded by PLIP DMS.11: 9 residues within 4Å: Chain A: M.228, G.233, K.234, K.254, V.256, K.257, P.258, K.288 Chain B: M.106 Ligand excluded by PLIP DMS.14: 6 residues within 4Å: Chain B: F.25, R.91, D.128 Chain D: F.25, R.91 Ligands: DMS.37 Ligand excluded by PLIP DMS.15: 9 residues within 4Å: Chain A: M.285 Chain B: S.39, H.59, I.86, W.110, D.150, L.294 Ligands: ZN.12, NAP.13 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain B: Y.209, Y.210, V.314, D.315 Ligand excluded by PLIP DMS.17: 7 residues within 4Å: Chain B: L.300, R.304, D.307 Chain C: G.167, T.169, D.237, K.257 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain B: D.307, F.310, Y.311 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: H.287 Chain B: G.98, Q.101, H.157, P.296 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain B: M.228, K.234, K.254, V.256, K.257, P.258, K.288 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: T.169, D.237 Chain C: E.303, R.304, D.307 Ligand excluded by PLIP DMS.24: 9 residues within 4Å: Chain C: C.37, S.39, H.59, I.86, W.110, D.150, L.294 Ligands: ZN.22, NAP.23 Ligand excluded by PLIP DMS.25: 7 residues within 4Å: Chain C: K.187, Y.209, Y.210, K.312, R.313, V.314, D.315 Ligand excluded by PLIP DMS.26: 8 residues within 4Å: Chain C: M.228, G.233, K.254, I.255, V.256, K.257, P.258, K.288 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain C: F.25, R.91, D.128 Ligands: DMS.3 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain C: E.143, S.317, V.320 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain C: E.139, V.309, F.310, K.312 Ligand excluded by PLIP DMS.30: 3 residues within 4Å: Chain C: H.53, M.55, V.115 Ligand excluded by PLIP DMS.31: 2 residues within 4Å: Chain C: D.307, Y.311 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain C: L.279, C.283 Chain D: I.49, M.106 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: T.169, D.237, K.257 Chain D: R.304, D.307 Ligand excluded by PLIP DMS.36: 8 residues within 4Å: Chain D: M.228, G.233, K.254, I.255, V.256, K.257, P.258, K.288 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: R.91 Chain D: F.25, R.91, D.128 Ligands: DMS.14 Ligand excluded by PLIP DMS.38: 10 residues within 4Å: Chain C: M.285 Chain D: C.37, S.39, H.59, I.86, W.110, D.150, L.294 Ligands: ZN.34, NAP.35 Ligand excluded by PLIP DMS.39: 4 residues within 4Å: Chain D: G.98, Y.99, Q.101, P.296 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain D: P.137, I.306, D.307, F.310, Y.311 Ligand excluded by PLIP DMS.41: 3 residues within 4Å: Chain D: E.160, D.163, K.291 Ligand excluded by PLIP DMS.42: 3 residues within 4Å: Chain D: F.310, Y.311, K.312 Ligand excluded by PLIP DMS.43: 6 residues within 4Å: Chain D: K.187, Y.209, Y.210, R.313, V.314, D.315 Ligand excluded by PLIP

Links

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Citation

Dinh, T. et al., Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network. Proteins (2022)

Release Date

2022-05-04

Peptides

Secondary-alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Secondary-alcohol dehydrogenase