SMTL ID : 6cxx.1

Horse liver E267H alcohol dehydrogenase complex with 3'-dephosphocoenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.46, H.67, C.174 Ligands: COD.3 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.9: 4 residues within 4Å: Chain B: C.46, H.67, C.174 Ligands: COD.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.46, B:H.67, B:C.174 ZN.10: 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 COD: DEPHOSPHO COENZYME A(Non-covalent)

COD.3: 29 residues within 4Å: Chain A: C.46, R.47, S.48, H.67, F.93, C.174, G.199, L.200, G.201, G.202, V.203, G.204, V.222, D.223, I.224, N.225, K.228, V.268, I.269, G.270, R.271, T.274, V.292, G.293, V.294, I.318 Chain B: L.309 Ligands: ZN.1, MRD.8 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.318, B:L.309 Hydrogen bonds: A:S.48, A:L.200, A:G.201, A:V.203, A:G.204, A:I.224, A:R.271, A:R.271, A:V.294 Water bridges: A:R.47, A:G.202, A:G.202, A:G.202, A:K.228, A:G.365, A:I.368, A:R.369, A:R.369 Salt bridges: A:R.47 COD.11: 30 residues within 4Å: Chain A: L.309 Chain B: C.46, R.47, S.48, H.67, F.93, L.116, C.174, G.199, L.200, G.201, G.202, V.203, G.204, V.222, D.223, I.224, N.225, K.228, V.268, I.269, G.270, R.271, T.274, V.292, G.293, V.294, I.318 Ligands: MRD.7, ZN.9 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.203, B:I.318, A:L.309 Hydrogen bonds: B:S.48, B:L.200, B:G.201, B:V.203, B:G.204, B:I.224, B:K.228, B:R.271, B:R.271, B:V.294 Water bridges: B:R.47, B:G.202, B:I.368, B:R.369, B:R.369 Salt bridges: B:R.47

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

MRD.4: 4 residues within 4Å: Chain A: D.343, I.346, T.347, H.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.346, A:T.347 Water bridges: A:V.349 MRD.5: 4 residues within 4Å: Chain A: R.218, T.238, E.239 Ligands: MPD.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.239 MRD.7: 5 residues within 4Å: Chain A: M.306, S.310 Chain B: L.116, S.117 Ligands: COD.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.116 MRD.8: 6 residues within 4Å: Chain A: L.116, S.117 Chain B: M.306, L.309, S.310 Ligands: COD.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.309, A:L.116, A:L.116 MRD.12: 4 residues within 4Å: Chain B: D.343, I.346, T.347, H.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.346, B:T.347

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 4 residues within 4Å: Chain A: R.218, T.238, E.239 Ligands: MRD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.239 Hydrogen bonds: A:T.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y.H. et al., Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Arch. Biochem. Biophys. (2018)

Release Date

2018-04-25

Peptides

Alcohol dehydrogenase E chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase E chain