SMTL ID : 2fzw.1

Structure of the binary complex of the E67L mutant of human glutathione-dependent formaldehyde dehydrogenase with NAD(H)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.96, A:C.99, A:C.102, A:C.110 ZN.2: 4 residues within 4Å: Chain A: C.44, T.46, H.66, C.173 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.44, A:H.66, A:C.173, H2O.1 ZN.6: 5 residues within 4Å: Chain B: C.96, G.97, C.99, C.102, C.110 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.96, B:C.99, B:C.102, B:C.110 ZN.7: 4 residues within 4Å: Chain B: C.44, T.46, H.66, C.173 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.44, B:H.66, B:C.173, H2O.21

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: K.83, D.86, K.158 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.86 Water bridges: A:K.83, A:K.83, A:K.83, A:K.158, A:K.158 Salt bridges: A:K.83, A:K.158 PO4.8: 2 residues within 4Å: Chain A: K.314 Chain B: K.314 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Water bridges: A:K.187, A:T.312, A:T.312, A:K.314, A:K.314, B:K.314, B:K.314, B:K.314 Salt bridges: A:K.314, B:K.314 PO4.9: 3 residues within 4Å: Chain B: K.83, D.86, K.158 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.86 Water bridges: B:K.83, B:K.83, B:D.86, B:K.158 Salt bridges: B:K.83, B:K.158

2 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: A.186, K.187, E.189, Y.263 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.186, A:Y.263 K.10: 4 residues within 4Å: Chain B: A.186, K.187, E.189, Y.263 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.186, B:Y.263

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.5: 24 residues within 4Å: Chain A: H.45, Y.92, C.173, T.177, G.198, G.200, G.201, V.202, V.221, D.222, I.223, N.224, K.227, C.267, I.268, G.269, V.273, V.291, G.292, V.293, T.316, A.317, F.318, R.368 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.177 Hydrogen bonds: A:H.45, A:L.199, A:V.202, A:I.223, A:I.268, A:V.291, A:V.293, A:F.318 Water bridges: A:G.200, A:G.200, A:G.201, A:N.224, A:K.227, A:K.227, A:N.270, A:N.270, A:S.366, A:R.368 Salt bridges: A:R.368 NAD.11: 20 residues within 4Å: Chain B: H.45, Y.49, G.198, G.200, G.201, V.202, V.221, D.222, I.223, N.224, K.227, C.267, I.268, G.269, V.273, V.291, G.292, V.293, A.294, R.368 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:G.200, B:G.200, B:G.201, B:V.202, B:I.223, B:V.291 Water bridges: B:H.45, B:G.203, B:K.227, B:I.268, B:N.270, B:N.270, B:N.270, B:G.364, B:R.368, B:R.368, B:R.368, B:R.368 Salt bridges: B:H.45, B:H.45, B:R.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanghani, P.C. et al., Structure-function relationships in human glutathione-dependent formaldehyde dehydrogenase. Role of Glu-67 and Arg-368 in the catalytic mechanism. Biochemistry (2006)

Release Date

2006-06-13

Peptides

Alcohol dehydrogenase class III chi chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase class III chi chain