SMTL ID : 5vn1.2 (1 other biounit)

horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.46, H.67, C.174 Ligands: NAI.3, NWH.4, NMH.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:C.46, A:H.67, A:C.174, NWH.4, NMH.5 ZN.2: 6 residues within 4Å: Chain A: C.97, G.98, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.7: 6 residues within 4Å: Chain B: C.46, S.48, H.67, C.174 Ligands: NAI.9, NWH.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.46, B:H.67, B:C.174, NWH.10 ZN.8: 5 residues within 4Å: Chain B: C.97, C.100, C.103, C.111, L.112 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111

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

NAI.3: 30 residues within 4Å: Chain A: C.46, R.47, S.48, H.51, C.174, T.178, G.199, L.200, G.201, G.202, V.203, D.223, I.224, N.225, K.228, V.268, I.269, G.270, R.271, V.292, G.293, V.294, A.317, I.318, F.319, L.362, R.369 Ligands: ZN.1, NWH.4, NMH.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.178, A:V.203 Hydrogen bonds: A:R.47, A:H.51, A:L.200, A:G.201, A:G.202, A:V.203, A:I.224, A:I.269, A:R.271, A:V.292, A:V.294, A:F.319 Water bridges: A:G.204, A:K.228, A:R.271, A:R.271, A:G.320, A:S.367, A:R.369, A:R.369 Salt bridges: A:R.47, A:R.369 NAI.9: 29 residues within 4Å: Chain B: C.46, R.47, S.48, H.51, C.174, T.178, G.199, L.200, G.201, G.202, V.203, D.223, I.224, N.225, K.228, V.268, I.269, G.270, R.271, V.292, G.293, V.294, A.317, I.318, F.319, L.362, R.369 Ligands: ZN.7, NWH.10 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:T.178, B:V.203 Hydrogen bonds: B:R.47, B:H.51, B:L.200, B:G.201, B:G.202, B:V.203, B:I.224, B:I.269, B:R.271, B:V.292, B:V.294, B:F.319 Water bridges: B:R.47, B:G.204, B:K.228, B:K.228, B:R.271, B:R.271, B:G.320, B:S.367, B:R.369, B:R.369 Salt bridges: B:R.47, B:R.369

2 x NWH: N-[(2S)-heptan-2-yl]formamide(Non-covalent)

NWH.4: 12 residues within 4Å: Chain A: C.46, S.48, L.57, H.67, F.93, L.116, L.141, C.174, I.318 Ligands: ZN.1, NAI.3, NMH.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.57, A:L.57, A:L.116, A:L.116, A:L.141, A:I.318 Hydrogen bonds: A:S.48 NWH.10: 12 residues within 4Å: Chain B: C.46, S.48, L.57, V.58, H.67, F.93, L.116, L.141, C.174, I.318 Ligands: ZN.7, NAI.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.57, B:L.116, B:L.116, B:L.141, B:I.318 Hydrogen bonds: B:S.48

1 x NMH: (R)-N-(1-METHYL-HEXYL)-FORMAMIDE(Covalent)

NMH.5: 15 residues within 4Å: Chain A: C.46, S.48, L.57, H.67, F.93, L.116, L.141, C.174, V.294, I.318 Chain B: M.306, L.309 Ligands: ZN.1, NAI.3, NWH.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.57, A:F.93, A:L.116, A:V.294, A:I.318 Hydrogen bonds: A:S.48

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 2 residues within 4Å: Chain A: K.338, F.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.340 Water bridges: A:K.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plapp, B.V. et al., Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry (2017)

Release Date

2017-05-10

Peptides

Alcohol dehydrogenase E chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Alcohol dehydrogenase E chain

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