SMTL ID : 4nfh.1

V207A Horse Liver Alcohol Dehydrogenase E complexed with NAD and 2,3,4,5,6-pentafluorobenzyl alcohol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 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: 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 Chain B: L.309 Ligands: ZN.1, PFB.4 26 PLIP interactions: 26 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: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 NAJ.10: 30 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, 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 24 PLIP interactions: 24 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: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:F.340 MRD.6: 3 residues within 4Å: Chain A: R.218, T.238, E.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.238 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: 4 residues within 4Å: Chain B: K.338, K.339, F.340, A.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yahashiri, A. et al., Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry (2014)

Release Date

2013-11-13

Peptides

Alcohol dehydrogenase E chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase E chain