SMTL ID : 1ma0.1

Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with NAD+ and dodecanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 6 residues within 4Å: Chain A: C.44, H.66, E.67, C.173, R.368 Ligands: DAO.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.44, A:H.66, A:E.67, A:C.173 ZN.8: 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.9: 6 residues within 4Å: Chain B: C.44, H.66, E.67, C.173, R.368 Ligands: DAO.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.44, B:H.66, B:E.67, B:C.173

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: A.186, K.187, E.189, Y.263 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.186, A:K.187, A:Y.263, H2O.5 K.10: 4 residues within 4Å: Chain B: A.186, K.187, E.189, Y.263 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.186, B:K.187, B:E.189, B:Y.263, H2O.8

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

PO4.4: 2 residues within 4Å: Chain A: K.314 Chain B: K.314 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:K.314, A:K.314, B:K.314 Salt bridges: A:K.314, B:K.314 PO4.5: 2 residues within 4Å: Chain A: K.83, K.158 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.83, A:K.158

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

NAD.6: 25 residues within 4Å: Chain A: H.45, T.46, Y.92, C.173, T.177, G.198, L.199, G.200, G.201, V.202, V.221, D.222, I.223, K.227, C.267, I.268, V.273, V.291, G.292, V.293, T.316, A.317, F.318, R.368 Ligands: DAO.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.177 Hydrogen bonds: A:T.46, 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.201, A:G.203, A:K.227, A:K.227, A:N.270, A:S.366, A:R.368, A:R.368, A:R.368 Salt bridges: A:H.45, A:R.368 NAD.11: 25 residues within 4Å: Chain B: H.45, T.46, C.173, T.177, G.198, L.199, G.200, G.201, V.202, V.221, D.222, I.223, N.224, K.227, C.267, I.268, V.273, V.291, G.292, V.293, T.316, A.317, F.318, R.368 Ligands: DAO.12 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.177 Hydrogen bonds: B:H.45, B:T.46, B:Y.92, B:T.177, B:G.200, B:G.200, B:V.202, B:I.223, B:I.268, B:V.291, B:V.293, B:F.318 Water bridges: B:H.45, B:G.201, B:G.203, B:K.227, B:N.270, B:N.270, B:N.270, B:S.366, B:R.368, B:R.368, B:R.368 Salt bridges: B:R.368

2 x DAO: LAURIC ACID(Non-covalent)

DAO.7: 13 residues within 4Å: Chain A: C.44, T.46, H.66, Y.92, I.93, L.109, Q.111, R.114, C.173, V.293 Chain B: K.283 Ligands: ZN.2, NAD.6 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.46, A:Y.92, A:I.93, A:L.109, A:V.293 Hydrogen bonds: A:Q.111 Water bridges: A:C.110, A:R.114 Salt bridges: A:R.114, B:K.283 DAO.12: 13 residues within 4Å: Chain A: K.283, T.309 Chain B: C.44, T.46, H.66, Y.92, Q.111, R.114, M.140, C.173, A.317 Ligands: ZN.9, NAD.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.317, A:T.309 Hydrogen bonds: B:Q.111 Salt bridges: B:R.114, A:K.283

Links

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Citation

Sanghani, P.C. et al., Human glutathione-dependent formaldehyde dehydrogenase. Structures of apo, binary, and inhibitory ternary complexes. Biochemistry (2002)

Release Date

2002-08-02

Peptides

Glutathione-dependent formaldehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutathione-dependent formaldehyde dehydrogenase

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