SMTL ID : 2gh5.1

Crystal Structure of human Glutathione Reductase complexed with a Fluoro-Analogue of the Menadione Derivative M5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: R.218, H.219 Ligands: PO4.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.218, A:H.219 PO4.2: 6 residues within 4Å: Chain A: A.195, R.218, H.219, R.224 Ligands: PO4.1, GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.218 Water bridges: A:H.219 Salt bridges: A:H.219, A:R.224 PO4.10: 3 residues within 4Å: Chain B: R.218, H.219 Ligands: PO4.11 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.224, B:R.224 Salt bridges: B:R.218, B:H.219 PO4.11: 6 residues within 4Å: Chain B: A.195, R.218, H.219, R.224 Ligands: PO4.10, GOL.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.218 Water bridges: B:A.195, B:H.219, B:R.224 Salt bridges: B:H.219, B:R.224

2 x ELI: 6-(3-METHYL-1,4-DIOXO-1,4-DIHYDRONAPHTHALEN-2-YL)HEXANOIC ACID(Covalent)

ELI.3: 14 residues within 4Å: Chain A: S.30, L.33, A.34, R.37, G.55, C.58, V.59, V.64, L.110, Y.114, T.339, R.347 Chain B: H.467 Ligands: GOL.18 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.33, A:A.34, A:V.59, A:V.59, A:L.110, A:L.110, A:Y.114, A:Y.114, A:T.339 Water bridges: A:R.347 Salt bridges: A:R.37, A:R.347 ELI.12: 13 residues within 4Å: Chain A: H.467 Chain B: S.30, L.33, A.34, R.37, G.55, C.58, V.59, V.64, L.110, Y.114, T.339, R.347 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.34, B:V.59, B:V.59, B:L.110, B:L.110, B:Y.114, B:Y.114, B:T.339 Hydrogen bonds: B:Y.114, B:Y.114 Salt bridges: B:R.37, B:R.347

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.4: 38 residues within 4Å: Chain A: I.26, G.27, G.28, G.29, S.30, G.31, V.49, E.50, S.51, H.52, K.53, G.56, T.57, C.58, V.61, G.62, C.63, K.66, G.128, H.129, A.130, A.155, T.156, G.157, S.177, Y.197, I.198, R.291, G.330, D.331, L.337, L.338, T.339, P.340, A.342, F.372 Chain B: H.467, P.468 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.57, A:I.198 Hydrogen bonds: A:G.28, A:S.30, A:S.30, A:G.31, A:S.51, A:T.57, A:T.57, A:T.57, A:C.58, A:K.66, A:A.130, A:A.130, A:D.331, A:L.337, A:T.339, A:T.339, A:T.339, B:H.467 Water bridges: A:G.29, A:G.32, A:K.53, A:G.56, A:H.129, A:T.156, A:G.157, A:G.158, A:G.158, A:G.158, A:A.342, B:H.467 pi-Stacking: A:Y.197 FAD.13: 39 residues within 4Å: Chain A: H.467, P.468 Chain B: I.26, G.27, G.28, G.29, S.30, G.31, V.49, E.50, S.51, H.52, K.53, G.56, T.57, C.58, V.61, G.62, C.63, K.66, G.128, H.129, A.130, A.155, T.156, G.157, S.177, Y.197, I.198, R.291, L.298, G.330, D.331, L.337, L.338, T.339, P.340, A.342, F.372 32 PLIP interactions: 30 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.57, B:I.198 Hydrogen bonds: B:G.28, B:S.30, B:S.30, B:G.31, B:G.32, B:S.51, B:T.57, B:T.57, B:C.58, B:K.66, B:A.130, B:A.130, B:Y.197, B:D.331, B:L.337, B:T.339, B:T.339, A:H.467 Water bridges: B:G.29, B:E.50, B:K.53, B:T.57, B:G.157, B:G.158, B:G.158, B:V.329, B:D.331, B:A.342, A:H.467 pi-Stacking: B:Y.197

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: G.194, A.195, G.196, A.288, I.289, G.290 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.195, A:G.196 Water bridges: A:Y.197 GOL.6: 2 residues within 4Å: Chain A: N.95, R.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.95 GOL.7: 2 residues within 4Å: Chain A: F.403, T.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.404, A:T.404 GOL.8: 3 residues within 4Å: Chain A: R.347 Chain B: T.476 Ligands: GOL.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.347, A:R.347, B:T.476 GOL.9: 5 residues within 4Å: Chain A: E.77, H.374, R.413, T.415, L.438 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.374, A:R.413, A:R.413 Water bridges: A:H.374 GOL.14: 4 residues within 4Å: Chain B: S.228, M.229, T.232, K.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.232, B:K.420, B:K.420 GOL.15: 4 residues within 4Å: Chain B: K.53, L.54, Q.115, R.127 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.54, B:Q.115, B:R.127, B:R.127 GOL.16: 6 residues within 4Å: Chain B: A.195, L.223, R.224, S.225, F.226 Ligands: PO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.195, B:R.224, B:S.225 GOL.17: 2 residues within 4Å: Chain B: F.403, T.404 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.109 Hydrogen bonds: B:T.404, B:T.404 GOL.18: 7 residues within 4Å: Chain A: P.340, I.343 Chain B: H.467, E.472, E.473 Ligands: ELI.3, GOL.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.472 GOL.19: 3 residues within 4Å: Chain A: T.476, R.478 Chain B: R.347 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.478, A:R.478, B:R.347, B:R.347 GOL.20: 8 residues within 4Å: Chain B: E.77, F.78, H.374, P.375, P.376, R.413, T.415, L.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.374, B:R.413, B:R.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauer, H. et al., A fluoro analogue of the menadione derivative 6-[2'-(3'-methyl)-1',4'-naphthoquinolyl]hexanoic acid is a suicide substrate of glutathione reductase. Crystal structure of the alkylated human enzyme. J.Am.Chem.Soc. (2006)

Release Date

2006-09-26

Peptides

glutathione reductase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

glutathione reductase, mitochondrial

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