SMTL ID : 1mc5.1

Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with S-(hydroxymethyl)glutathione and NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.97, G.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.2: 6 residues within 4Å: Chain A: C.45, T.47, H.67, C.174 Ligands: NAD.6, AHE.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.45, A:H.67, A:C.174 ZN.8: 5 residues within 4Å: Chain B: C.97, G.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111 ZN.9: 5 residues within 4Å: Chain B: C.45, H.67, E.68, C.174, R.369 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.45, B:H.67, B:E.68, B:C.174

1 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: A.187, K.188, E.190, Y.264 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.187, A:K.188, A:E.190, A:Y.264, H2O.5

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

PO4.4: 2 residues within 4Å: Chain A: K.315 Chain B: K.315 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:T.313, A:K.315 Salt bridges: A:K.315, B:K.315 PO4.5: 3 residues within 4Å: Chain A: K.84, D.87, K.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.84, A:K.159 PO4.10: 3 residues within 4Å: Chain B: K.84, D.87, K.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.87 Water bridges: B:K.84 Salt bridges: B:K.84, B:K.159

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

NAD.6: 28 residues within 4Å: Chain A: C.45, H.46, T.47, Y.93, C.174, T.178, G.199, L.200, G.201, G.202, V.203, V.222, D.223, I.224, K.228, C.268, I.269, G.270, V.274, V.292, G.293, V.294, T.317, A.318, F.319, R.369 Ligands: ZN.2, AHE.7 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.178, A:V.203 Hydrogen bonds: A:H.46, A:G.199, A:L.200, A:G.202, A:V.203, A:I.224, A:K.228, A:K.228, A:I.269, A:V.292, A:V.294, A:F.319 Water bridges: A:R.369, A:R.369 Salt bridges: A:H.46, A:R.369 NAD.11: 26 residues within 4Å: Chain B: H.46, T.47, Y.93, C.174, T.178, G.199, L.200, G.201, G.202, V.203, V.222, D.223, I.224, N.225, K.228, C.268, I.269, G.270, V.274, V.292, G.293, V.294, T.317, A.318, F.319, R.369 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:T.178 Hydrogen bonds: B:T.47, B:Y.93, B:T.178, B:L.200, B:G.201, B:V.203, B:I.224, B:I.269, B:V.292, B:V.294, B:F.319 Water bridges: B:H.46, B:H.46, B:L.200, B:G.202, B:G.202, B:G.204, B:K.228, B:K.228 Salt bridges: B:H.46, B:H.46, B:R.369

1 x AHE: 2-AMINO-4-[1-CARBOXYMETHYL-CARBAMOYL)-2-HYDROXYMETHYLSULFANYL-ETHYLCARBAMOYL]-BUTYRIC ACID(Non-covalent)

AHE.7: 16 residues within 4Å: Chain A: C.45, T.47, D.56, P.57, E.58, H.67, Y.93, I.94, R.115, C.174, V.294, A.318 Chain B: F.306, V.309 Ligands: ZN.2, NAD.6 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.294, B:F.306 Hydrogen bonds: A:E.58, A:E.58, A:E.58 Water bridges: A:Q.112 Salt bridges: A:R.115, B:K.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanghani, P.C. et al., Human glutathione-dependent formaldehyde dehydrogenase.Structural changes associated with Ternary Complex formation. Biochemistry (2002)

Release Date

2003-03-04

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