SMTL ID : 8con.1

Crystal structure of alcohol dehydrogenase from Arabidopsis thaliana in complex with NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.47, H.69, E.70, C.177, R.372 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.47, A:H.69, A:E.70, A:C.177 ZN.2: 6 residues within 4Å: Chain A: C.99, G.100, C.102, C.105, C.113, D.114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.105, A:C.113 ZN.20: 5 residues within 4Å: Chain B: C.47, H.69, E.70, C.177, R.372 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.47, B:H.69, B:E.70, B:C.177 ZN.21: 6 residues within 4Å: Chain B: C.99, G.100, C.102, C.105, C.113, D.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.99, B:C.102, B:C.105, B:C.113

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 23 residues within 4Å: Chain A: H.48, C.177, T.181, G.202, L.203, G.204, A.205, V.206, D.226, F.227, N.228, R.231, C.271, T.272, G.273, S.274, V.295, G.296, V.297, T.320, F.321, F.322 Ligands: PG4.9 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.181 Hydrogen bonds: A:L.203, A:G.204, A:V.206, A:F.227, A:R.231, A:T.272, A:S.274, A:S.274, A:V.297, A:T.320, A:F.322 Water bridges: A:H.48, A:A.205, A:G.207, A:R.372, A:R.372 Salt bridges: A:H.48 pi-Stacking: A:F.227 NAI.22: 23 residues within 4Å: Chain B: H.48, C.177, T.181, G.202, L.203, G.204, A.205, V.206, D.226, F.227, N.228, R.231, C.271, T.272, G.273, S.274, V.295, G.296, V.297, T.320, F.321, F.322 Ligands: PG4.28 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.181 Hydrogen bonds: B:L.203, B:G.204, B:V.206, B:F.227, B:R.231, B:T.272, B:S.274, B:S.274, B:V.297, B:T.320, B:F.322 Water bridges: B:H.48, B:H.48, B:A.205, B:G.207, B:R.372, B:R.372 Salt bridges: B:H.48 pi-Stacking: B:F.227

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: K.193, Q.196, R.267, W.289 Chain B: E.109 Ligands: PEG.15 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:E.108, A:R.267, A:R.267 Hydrogen bonds: A:Q.196 Salt bridges: A:K.193, A:R.267 SO4.5: 4 residues within 4Å: Chain A: S.274, V.275, Q.276, D.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.275, A:Q.276 SO4.6: 5 residues within 4Å: Chain A: K.191, K.318 Chain B: K.191, K.318 Ligands: SO4.25 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Water bridges: A:K.191, A:K.318, A:K.318, B:K.191, B:K.191, B:K.318, B:K.318 Salt bridges: A:K.191, A:K.318, B:K.191, B:K.318 SO4.7: 2 residues within 4Å: Chain A: Y.338, M.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.338, A:M.339 Water bridges: A:K.341 Salt bridges: A:K.341 SO4.8: 3 residues within 4Å: Chain A: H.249, D.250, K.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.250, A:K.251 Salt bridges: A:H.249, A:K.251 SO4.23: 6 residues within 4Å: Chain A: E.109 Chain B: K.193, Q.196, R.267, W.289 Ligands: PEG.34 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.196 Water bridges: B:R.267, B:R.267, A:E.108 Salt bridges: B:K.193, B:R.267 SO4.24: 4 residues within 4Å: Chain B: S.274, V.275, Q.276, D.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.275, B:Q.276, B:D.302 SO4.25: 5 residues within 4Å: Chain A: K.191, K.318 Chain B: K.191, K.318 Ligands: SO4.6 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Water bridges: B:K.191, B:K.318, B:K.318, A:K.191, A:K.191, A:K.318, A:K.318 Salt bridges: B:K.191, B:K.318, A:K.191, A:K.318 SO4.26: 2 residues within 4Å: Chain B: Y.338, M.339 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.338, B:M.339 Water bridges: B:K.341 Salt bridges: B:K.341 SO4.27: 3 residues within 4Å: Chain B: H.249, D.250, K.251 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.250, B:K.251 Salt bridges: B:H.249, B:K.251

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

PG4.9: 9 residues within 4Å: Chain A: T.49, Y.52, M.112, I.118, V.297, F.321 Chain B: M.309, L.312 Ligands: NAI.3 No protein-ligand interaction detected (PLIP) PG4.10: 6 residues within 4Å: Chain A: P.64, E.130, S.131, P.139, I.140, Y.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.131 PG4.11: 5 residues within 4Å: Chain A: V.78, G.79, E.80, V.82, T.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.78 Water bridges: A:G.81, A:G.81 PG4.28: 9 residues within 4Å: Chain A: M.309, L.312 Chain B: T.49, Y.52, M.112, I.118, V.297, F.321 Ligands: NAI.22 No protein-ligand interaction detected (PLIP) PG4.29: 6 residues within 4Å: Chain B: P.64, E.130, S.131, P.139, I.140, Y.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.131 PG4.30: 5 residues within 4Å: Chain B: V.78, G.79, E.80, V.82, T.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.78 Water bridges: B:G.81, B:G.81

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 1 residues within 4Å: Chain A: T.83 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain A: E.108, N.188, N.324, D.330 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.188 PEG.14: 4 residues within 4Å: Chain A: I.216, Y.325, K.337, E.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.337, A:E.342 PEG.15: 8 residues within 4Å: Chain A: Q.196, D.266, W.289 Chain B: R.103, H.106, S.107 Ligands: SO4.4, PEG.16 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.103, A:Q.196 Water bridges: B:E.108, B:E.108, B:E.108 PEG.16: 6 residues within 4Å: Chain A: K.193, K.194, G.195, Q.196 Ligands: PEG.15, EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.195 PEG.17: 2 residues within 4Å: Chain A: E.357, K.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.357 PEG.31: 1 residues within 4Å: Chain B: T.83 No protein-ligand interaction detected (PLIP) PEG.32: 4 residues within 4Å: Chain B: E.108, N.188, N.324, D.330 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.188 PEG.33: 4 residues within 4Å: Chain B: I.216, Y.325, K.337, E.342 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.337, B:E.342 PEG.34: 8 residues within 4Å: Chain A: R.103, H.106, S.107 Chain B: Q.196, D.266, W.289 Ligands: SO4.23, PEG.35 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.103, B:Q.196 Water bridges: A:E.108, A:E.108, A:E.108 PEG.35: 6 residues within 4Å: Chain B: K.193, K.194, G.195, Q.196 Ligands: PEG.34, EDO.37 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.195 PEG.36: 2 residues within 4Å: Chain B: E.357, K.360 No protein-ligand interaction detected (PLIP)

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

EDO.18: 5 residues within 4Å: Chain A: G.195, S.197, D.266 Chain B: R.103 Ligands: PEG.16 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.103, A:S.197 Water bridges: A:T.261 EDO.19: 2 residues within 4Å: Chain A: Q.254, E.283 No protein-ligand interaction detected (PLIP) EDO.37: 5 residues within 4Å: Chain A: R.103 Chain B: G.195, S.197, D.266 Ligands: PEG.35 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.103, B:S.197 Water bridges: B:T.261 EDO.38: 2 residues within 4Å: Chain B: Q.254, E.283 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meloni, M. et al., Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. Plant J. (2024)

Release Date

2024-02-21

Peptides

Alcohol dehydrogenase class-P: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alcohol dehydrogenase class-P