SMTL ID : 3djj.1

Catalytic cycle of human glutathione reductase near 1 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 3 residues within 4Å: Chain A: A.34, R.37, R.347 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Water bridges: A:L.33, A:R.38, A:R.38, A:R.347, A:R.347, A:R.347, B:R.478, B:R.478 Salt bridges: A:R.37, A:R.347 PO4.2: 2 residues within 4Å: Chain A: R.218, H.219 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.224 Salt bridges: A:R.218, A:H.219 PO4.3: 2 residues within 4Å: Chain A: R.38, R.347 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:R.38, A:R.347, A:R.347, B:D.461, B:R.478, B:R.478 Salt bridges: A:R.38, A:R.347 PO4.4: 4 residues within 4Å: Chain A: T.176, D.178, G.179, Q.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.182 Water bridges: A:G.179, A:G.179, A:Q.182, A:Q.182 PO4.5: 7 residues within 4Å: Chain A: H.52, K.53, L.54, N.111, Q.115, R.127 Ligands: GOL.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.54, A:N.111, A:Q.115 Water bridges: A:H.52 Salt bridges: A:R.127 PO4.20: 3 residues within 4Å: Chain B: A.34, R.37, R.347 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Water bridges: B:L.33, B:R.38, B:R.38, B:R.347, B:R.347, B:R.347, A:R.478, A:R.478 Salt bridges: B:R.37, B:R.347 PO4.21: 2 residues within 4Å: Chain B: R.218, H.219 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.224 Salt bridges: B:R.218, B:H.219 PO4.22: 2 residues within 4Å: Chain B: R.38, R.347 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:R.38, B:R.347, B:R.347, A:D.461, A:R.478, A:R.478 Salt bridges: B:R.38, B:R.347 PO4.23: 4 residues within 4Å: Chain B: T.176, D.178, G.179, Q.182 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.182 Water bridges: B:G.179, B:G.179, B:Q.182, B:Q.182 PO4.24: 7 residues within 4Å: Chain B: H.52, K.53, L.54, N.111, Q.115, R.127 Ligands: GOL.37 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.54, B:N.111, B:Q.115 Water bridges: B:H.52 Salt bridges: B:R.127

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

SO4.6: 2 residues within 4Å: Chain A: K.120, S.121 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.120, A:S.121, A:S.121, A:H.122 SO4.7: 2 residues within 4Å: Chain A: N.320 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.316, A:N.320 SO4.8: 3 residues within 4Å: Chain A: T.404, K.414, T.415 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.404 SO4.9: 2 residues within 4Å: Chain A: D.385, E.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.385 Water bridges: A:T.383 SO4.25: 2 residues within 4Å: Chain B: K.120, S.121 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.121, B:H.122 SO4.26: 2 residues within 4Å: Chain B: N.320 Ligands: GOL.33 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.316, B:N.320 SO4.27: 3 residues within 4Å: Chain B: T.404, K.414, T.415 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.415 Water bridges: B:T.404 SO4.28: 2 residues within 4Å: Chain B: D.385, E.386 No protein-ligand interaction detected (PLIP)

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

FAD.10: 39 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, I.198, R.291, N.294, L.298, G.330, D.331, L.337, L.338, T.339, P.340, F.372 Chain B: H.467, P.468 Ligands: NDP.11 31 PLIP interactions: 29 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.57, A:I.198 Hydrogen bonds: A:S.30, A:G.31, A:S.51, 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:S.51, A:H.52, A:K.53, A:G.56, A:T.57, A:T.156, A:G.157, A:G.157, A:G.158, A:N.294, A:A.342, B:H.467 FAD.29: 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, I.198, R.291, N.294, L.298, G.330, D.331, L.337, L.338, T.339, P.340, F.372 Ligands: NDP.30 30 PLIP interactions: 28 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.57, B:I.198 Hydrogen bonds: B:S.30, B:G.31, B:S.51, B:H.52, B:T.57, B:T.57, B:T.57, B:C.58, B:K.66, B:A.130, B:A.130, B:D.331, B:L.337, B:T.339, B:T.339, A:H.467 Water bridges: B:G.29, B:G.32, B:S.51, B:K.53, B:G.56, B:G.157, B:G.157, B:G.158, B:N.294, B:D.331, B:A.342, A:H.467

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.11: 20 residues within 4Å: Chain A: K.66, G.194, A.195, G.196, Y.197, I.198, E.201, R.218, H.219, R.224, A.288, I.289, G.290, R.291, L.337, L.338, V.370, F.372 Ligands: FAD.10, GOL.12 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:Y.197, A:Y.197, A:I.198 Hydrogen bonds: A:K.66, A:A.195, A:G.196, A:Y.197, A:I.198, A:E.201, A:G.290, A:L.337 Water bridges: A:G.196, A:A.199, A:R.218, A:R.218, A:R.218, A:R.218, A:R.218, A:H.219, A:R.224, A:R.224, A:R.224, A:Q.250, A:I.289, A:R.291, A:T.369, A:V.370 Salt bridges: A:R.218, A:H.219, A:R.224 pi-Cation interactions: A:R.218, A:R.218 NDP.30: 20 residues within 4Å: Chain B: K.66, G.194, A.195, G.196, Y.197, I.198, E.201, R.218, H.219, R.224, A.288, I.289, G.290, R.291, L.337, L.338, V.370, F.372 Ligands: FAD.29, GOL.31 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:Y.197, B:Y.197, B:I.198 Hydrogen bonds: B:K.66, B:A.195, B:G.196, B:Y.197, B:I.198, B:E.201, B:G.290, B:L.337, B:T.369 Water bridges: B:G.196, B:A.199, B:R.218, B:R.218, B:R.218, B:R.218, B:R.218, B:H.219, B:R.224, B:R.224, B:R.224, B:Q.250, B:I.289, B:R.291, B:V.370 Salt bridges: B:R.218, B:H.219, B:R.224 pi-Cation interactions: B:R.218, B:R.218

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: Y.197, A.336, L.338 Ligands: NDP.11, GOL.19 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: S.228, M.229, K.420 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: N.320, K.324, G.325, Y.327, R.352, L.353 Ligands: SO4.7 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: Y.364, N.365, N.366, I.367, V.380, G.381 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain A: K.102, A.105 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: L.246, M.265, T.267, T.277 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: L.54, N.111, A.112, Q.115 Ligands: PO4.5 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain A: Y.197, S.225, F.226, T.369, T.379, T.383 Ligands: GOL.12 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: Y.197, A.336, L.338 Ligands: NDP.30, GOL.38 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain B: S.228, M.229, K.420 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain B: N.320, K.324, G.325, Y.327, R.352, L.353 Ligands: SO4.26 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain B: Y.364, N.365, N.366, I.367, V.380, G.381 Ligand excluded by PLIP GOL.35: 2 residues within 4Å: Chain B: K.102, A.105 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: L.246, M.265, T.267, T.277 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain B: L.54, N.111, A.112, Q.115 Ligands: PO4.24 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain B: Y.197, S.225, F.226, T.369, T.379, T.383 Ligands: GOL.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berkholz, D.S. et al., Catalytic cycle of human glutathione reductase near 1 A resolution. J.Mol.Biol. (2008)

Release Date

2008-08-05

Peptides

Glutathione reductase, mitochondrial precursor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutathione reductase, mitochondrial precursor

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