SMTL ID : 4dwv.1

Horse alcohol dehydrogenase complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.46, S.48, H.67, C.174 Ligands: NAJ.3, PFB.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.46, A:H.67, A:C.174 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.8: 6 residues within 4Å: Chain B: C.46, S.48, H.67, C.174 Ligands: NAJ.10, PFB.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.46, B:H.67, B:C.174 ZN.9: 6 residues within 4Å: Chain B: C.97, G.98, 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 NAJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)(Non-covalent)

NAJ.3: 31 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, V.222, 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 Chain B: L.309 Ligands: ZN.1, PFB.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.178, A:V.203 Hydrogen bonds: A:R.47, A:H.51, A:T.178, 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:R.47, A:R.47, A:G.204, A:R.271, A:G.320, A:S.367, A:R.369, A:R.369 Salt bridges: A:R.47, A:R.369 NAJ.10: 31 residues within 4Å: Chain A: L.309 Chain B: C.46, R.47, S.48, H.51, C.174, T.178, G.199, L.200, G.201, G.202, V.203, V.222, 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.8, PFB.11 25 PLIP interactions: 25 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:R.47, B:G.204, B:K.228, 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 PFB: 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL(Non-covalent)

PFB.4: 14 residues within 4Å: Chain A: C.46, S.48, L.57, H.67, F.93, L.116, F.140, L.141, C.174, V.294, I.318 Chain B: L.309 Ligands: ZN.1, NAJ.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.93 Hydrogen bonds: A:S.48 PFB.11: 14 residues within 4Å: Chain A: L.309 Chain B: C.46, S.48, L.57, H.67, F.93, L.116, F.140, L.141, C.174, V.294, I.318 Ligands: ZN.8, NAJ.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.93 Hydrogen bonds: B:S.48

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

MRD.5: 4 residues within 4Å: Chain A: K.338, K.339, F.340, A.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.339 MRD.6: 3 residues within 4Å: Chain A: R.218, T.238, E.239 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.218 MRD.7: 5 residues within 4Å: Chain A: K.168, D.343, I.346, T.347, H.348 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.346 Hydrogen bonds: A:I.346 Water bridges: A:T.347 MRD.12: 3 residues within 4Å: Chain B: K.338, K.339, A.341 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.341 Hydrogen bonds: B:K.338 Water bridges: B:A.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plapp, B.V. et al., Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD(+) and Fluoroalcohols Define Strained Michaelis Complexes. Biochemistry (2012)

Release Date

2012-04-11

Peptides

Alcohol dehydrogenase E chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase E chain

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