SMTL ID : 1xa8.3 (2 other biounits)

Crystal Structure Analysis of Glutathione-dependent formaldehyde-activating enzyme (Gfa)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.33, C.35, C.101, C.104 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.33, A:C.35, A:C.101, A:C.104 ZN.4: 4 residues within 4Å: Chain B: C.33, C.35, C.101, C.104 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.33, B:C.35, B:C.101, B:C.104 ZN.9: 4 residues within 4Å: Chain C: C.33, C.35, C.101, C.104 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.33, C:C.35, C:C.101, C:C.104 ZN.13: 4 residues within 4Å: Chain D: C.33, C.35, C.101, C.104 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.33, D:C.35, D:C.101, D:C.104

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: S.7, G.8, K.10 Chain C: K.20 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.8 Salt bridges: A:K.10, C:K.20 Water bridges: A:R.163 SO4.5: 3 residues within 4Å: Chain A: P.177 Chain B: R.161, R.165 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.165 Water bridges: B:R.165, B:R.165 SO4.6: 4 residues within 4Å: Chain B: A.14, K.20, Q.69, E.128 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.20 SO4.10: 5 residues within 4Å: Chain A: K.20, D.133 Chain C: S.7, G.8, K.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.133, C:G.8 Salt bridges: A:K.20 SO4.14: 4 residues within 4Å: Chain D: A.14, K.20, Q.69, E.128 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.20 Water bridges: D:D.133

4 x GSH: GLUTATHIONE(Non-covalent)

GSH.3: 10 residues within 4Å: Chain A: C.56, T.57, K.58, A.94, P.95, I.96, R.98, F.143, S.146, E.149 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.57, A:K.58, A:K.58, A:K.58, A:I.96, A:R.98, A:S.146, A:S.146, A:E.149 Salt bridges: A:K.58 GSH.7: 10 residues within 4Å: Chain B: C.56, T.57, K.58, A.94, P.95, I.96, R.98, F.143, S.146, E.149 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.143 Hydrogen bonds: B:T.57, B:I.96, B:R.98, B:S.146, B:S.146 Salt bridges: B:K.58 GSH.11: 10 residues within 4Å: Chain C: C.56, T.57, K.58, A.94, P.95, I.96, R.98, F.143, S.146, E.149 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:K.58 Hydrogen bonds: C:T.57, C:K.58, C:K.58, C:I.96, C:S.146, C:S.146 Salt bridges: C:K.58, C:R.98 Water bridges: C:R.98 GSH.15: 9 residues within 4Å: Chain D: C.56, T.57, K.58, P.95, I.96, R.98, F.143, S.146, E.149 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.143 Hydrogen bonds: D:T.57, D:I.96, D:S.146, D:E.149 Salt bridges: D:K.58, D:R.98

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: H.50, L.179, A.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.50, B:P.118 GOL.12: 3 residues within 4Å: Chain C: Q.47, V.73, G.74 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.47, C:G.74 GOL.16: 3 residues within 4Å: Chain D: P.118, L.179, A.182 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.50, D:A.182 Water bridges: D:H.186

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Neculai, A.M. et al., A dynamic zinc redox switch. J.Biol.Chem. (2005)

Release Date

2004-11-23

Peptides

Glutathione-dependent formaldehyde-activating enzyme: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Glutathione-dependent formaldehyde-activating enzyme

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