SMTL ID : 5v36.2 (1 other biounit)

1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.13, G.14, G.16, S.17, G.18, F.36, E.37, G.38, K.39, G.43, T.44, C.45, V.48, G.49, C.50, K.53, G.116, Y.117, A.118, A.141, T.142, G.143, S.160, Y.180, I.181, R.266, F.273, G.305, D.306, E.312, L.313, T.314, P.315 Chain B: H.442, P.443 35 PLIP interactions: 33 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.44, A:I.181 Hydrogen bonds: A:G.15, A:S.17, A:S.17, A:G.18, A:G.38, A:K.39, A:T.44, A:T.44, A:T.44, A:C.45, A:K.53, A:A.118, A:A.118, A:Y.180, A:D.306, A:E.312, A:T.314, A:T.314, B:H.442 Water bridges: A:G.16, A:G.19, A:K.39, A:Q.40, A:G.43, A:G.143, A:G.144, A:G.144, A:G.144, A:V.307, A:A.317, B:H.442 pi-Stacking: A:Y.180, A:Y.180 FAD.27: 36 residues within 4Å: Chain A: H.442, P.443 Chain B: I.13, G.14, G.16, S.17, G.18, F.36, E.37, G.38, K.39, G.43, T.44, C.45, V.48, G.49, C.50, K.53, G.116, Y.117, A.118, A.141, T.142, G.143, S.160, Y.180, I.181, R.266, F.273, G.305, D.306, E.312, L.313, T.314, P.315, A.317 36 PLIP interactions: 34 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.44, B:I.181, B:I.181 Hydrogen bonds: B:G.15, B:S.17, B:S.17, B:G.18, B:G.38, B:K.39, B:T.44, B:T.44, B:C.45, B:K.53, B:A.118, B:A.118, B:D.306, B:E.312, B:T.314, B:T.314, B:T.314, A:H.442 Water bridges: B:G.16, B:G.19, B:K.39, B:K.39, B:Q.40, B:G.43, B:T.44, B:G.143, B:G.144, B:D.306, B:V.307, B:A.317, A:H.442 pi-Stacking: B:Y.180, B:Y.180 FAD.50: 35 residues within 4Å: Chain C: I.13, G.14, G.16, S.17, G.18, F.36, E.37, G.38, K.39, G.43, T.44, C.45, V.48, G.49, C.50, K.53, G.116, Y.117, A.118, A.141, T.142, G.143, S.160, Y.180, I.181, R.266, F.273, G.305, D.306, E.312, L.313, T.314, P.315 Chain D: H.442, P.443 34 PLIP interactions: 32 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.44, C:I.181 Hydrogen bonds: C:G.15, C:S.17, C:S.17, C:G.18, C:G.38, C:K.39, C:T.44, C:T.44, C:C.45, C:K.53, C:A.118, C:A.118, C:D.306, C:E.312, C:T.314, C:T.314, C:T.314, D:H.442 Water bridges: C:G.16, C:G.19, C:K.39, C:Q.40, C:G.43, C:T.44, C:G.143, C:G.144, C:D.306, C:V.307, C:A.317, D:H.442 pi-Stacking: C:Y.180, C:Y.180 FAD.76: 36 residues within 4Å: Chain C: H.442, P.443 Chain D: I.13, G.14, G.16, S.17, G.18, F.36, E.37, G.38, K.39, G.43, T.44, C.45, V.48, G.49, C.50, K.53, G.116, Y.117, A.118, A.141, T.142, G.143, S.160, Y.180, I.181, R.266, F.273, G.305, D.306, E.312, L.313, T.314, P.315, A.317 37 PLIP interactions: 35 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:T.44, D:I.181, D:I.181 Hydrogen bonds: D:G.15, D:S.17, D:S.17, D:G.18, D:G.38, D:K.39, D:T.44, D:T.44, D:T.44, D:C.45, D:K.53, D:A.118, D:A.118, D:Y.180, D:D.306, D:E.312, D:T.314, D:T.314, C:H.442 Water bridges: D:G.16, D:G.19, D:K.39, D:K.39, D:Q.40, D:G.43, D:G.143, D:G.144, D:G.144, D:G.144, D:V.307, D:A.317, C:H.442 pi-Stacking: D:Y.180, D:Y.180

4 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 6 residues within 4Å: Chain A: C.45, V.46, V.51, I.98, Y.102 Chain B: H.442 No protein-ligand interaction detected (PLIP) BME.28: 5 residues within 4Å: Chain A: H.442 Chain B: C.45, V.46, V.51, I.98 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.102 BME.51: 6 residues within 4Å: Chain C: C.45, V.46, V.51, I.98, Y.102 Chain D: H.442 No protein-ligand interaction detected (PLIP) BME.77: 5 residues within 4Å: Chain C: H.442 Chain D: C.45, V.46, V.51, I.98 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Y.102, D:Y.102

16 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: F.82 Ligands: EPE.26 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: I.158, T.159, G.162 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: G.265, R.266 Ligands: SO4.13 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.21, N.24, R.322 Ligands: SO4.16 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain A: K.54, Y.58 Chain B: M.381, P.443, T.444 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: K.340, D.341 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: R.204, K.211 Ligands: SO4.34 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain B: T.372, V.373 Ligands: SO4.46 Ligand excluded by PLIP CL.52: 2 residues within 4Å: Chain C: F.82 Ligands: EPE.75 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain C: I.158, T.159, G.162 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain C: G.265, R.266 Ligands: SO4.62 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain C: A.21, N.24, R.322 Ligands: SO4.65 Ligand excluded by PLIP CL.78: 5 residues within 4Å: Chain C: K.54, Y.58 Chain D: M.381, P.443, T.444 Ligand excluded by PLIP CL.79: 2 residues within 4Å: Chain D: K.340, D.341 Ligand excluded by PLIP CL.80: 3 residues within 4Å: Chain D: R.204, K.211 Ligands: SO4.83 Ligand excluded by PLIP CL.81: 3 residues within 4Å: Chain D: T.372, V.373 Ligands: SO4.95 Ligand excluded by PLIP

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

SO4.7: 3 residues within 4Å: Chain A: K.222, H.227, L.228 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: Y.94, R.97 Chain B: T.379, A.384, R.389 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: A.384, R.389 Chain B: Y.94, R.97 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: A.178, R.201, R.202, R.207 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: N.370, G.400, E.401 Chain C: K.332 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: R.453 Chain B: N.24, R.25, M.28, N.109, R.322 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: G.179, Y.180 Ligands: CL.5 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain A: H.190 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: D.203, R.204, R.207, K.211 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain A: N.24, R.25, M.28, R.322 Chain B: R.453 Ligands: CL.6 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: T.379, R.389 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: V.318, K.319, R.322 Ligands: SO4.19 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: R.25, Q.323 Ligands: SO4.18 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain A: K.427 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: D.283, S.284 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: V.318, R.322 Chain B: T.451 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain B: A.178, R.201, R.207 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain B: D.203, R.204, R.207, K.211 Ligands: CL.31, SO4.39 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain A: R.453 Chain B: R.25, R.322 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain B: H.145, L.147, K.271 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain B: H.190, H.227 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: K.222, H.227, L.228 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: R.202, R.207 Ligands: SO4.34 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain B: I.158, T.159, D.161, G.162, E.165 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: G.400, E.401 Chain D: K.332 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain B: D.283, S.284 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain B: G.179, Y.180 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain A: T.451 Chain B: R.322 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain B: R.389 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain B: E.359, V.373, R.375 Ligands: CL.32 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain C: K.222, H.227, L.228 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain C: Y.94, R.97 Chain D: T.379, A.384, R.389 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain C: A.384, R.389 Chain D: Y.94, R.97 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain C: A.178, R.201, R.202, R.207 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain A: K.332 Chain C: N.370, G.400, E.401 Ligand excluded by PLIP SO4.61: 6 residues within 4Å: Chain C: R.453 Chain D: N.24, R.25, M.28, N.109, R.322 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain C: G.179, Y.180 Ligands: CL.54 Ligand excluded by PLIP SO4.63: 1 residues within 4Å: Chain C: H.190 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain C: D.203, R.204, R.207, K.211 Ligand excluded by PLIP SO4.65: 6 residues within 4Å: Chain C: N.24, R.25, M.28, R.322 Chain D: R.453 Ligands: CL.55 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain C: T.379, R.389 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain C: V.318, K.319, R.322 Ligands: SO4.68 Ligand excluded by PLIP SO4.68: 3 residues within 4Å: Chain C: R.25, Q.323 Ligands: SO4.67 Ligand excluded by PLIP SO4.69: 1 residues within 4Å: Chain C: K.427 Ligand excluded by PLIP SO4.70: 2 residues within 4Å: Chain C: D.283, S.284 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain C: V.318, R.322 Chain D: T.451 Ligand excluded by PLIP SO4.82: 3 residues within 4Å: Chain D: A.178, R.201, R.207 Ligand excluded by PLIP SO4.83: 6 residues within 4Å: Chain D: D.203, R.204, R.207, K.211 Ligands: CL.80, SO4.88 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain C: R.453 Chain D: R.25, R.322 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain D: H.145, L.147, K.271 Ligand excluded by PLIP SO4.86: 2 residues within 4Å: Chain D: H.190, H.227 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain D: K.222, H.227, L.228 Ligand excluded by PLIP SO4.88: 3 residues within 4Å: Chain D: R.202, R.207 Ligands: SO4.83 Ligand excluded by PLIP SO4.89: 5 residues within 4Å: Chain D: I.158, T.159, D.161, G.162, E.165 Ligand excluded by PLIP SO4.90: 3 residues within 4Å: Chain B: K.332 Chain D: G.400, E.401 Ligand excluded by PLIP SO4.91: 2 residues within 4Å: Chain D: D.283, S.284 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain D: G.179, Y.180 Ligand excluded by PLIP SO4.93: 2 residues within 4Å: Chain C: T.451 Chain D: R.322 Ligand excluded by PLIP SO4.94: 1 residues within 4Å: Chain D: R.389 Ligand excluded by PLIP SO4.95: 4 residues within 4Å: Chain D: E.359, V.373, R.375 Ligands: CL.81 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 6 residues within 4Å: Chain A: K.271, G.272, F.273, N.274, L.275, E.276 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.272, A:N.274, A:E.276 Water bridges: A:L.275, A:L.275 GOL.24: 3 residues within 4Å: Chain A: H.145, L.147, K.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.271 GOL.25: 2 residues within 4Å: Chain A: D.291, A.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.292 GOL.47: 6 residues within 4Å: Chain B: K.271, G.272, F.273, N.274, L.275, E.276 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.272, B:N.274, B:E.276 Water bridges: B:N.274, B:L.275, B:L.275 GOL.48: 2 residues within 4Å: Chain B: D.291, A.292 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.292 Water bridges: B:D.291, B:D.291 GOL.72: 6 residues within 4Å: Chain C: K.271, G.272, F.273, N.274, L.275, E.276 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.272, C:N.274, C:E.276 Water bridges: C:L.275, C:L.275 GOL.73: 3 residues within 4Å: Chain C: H.145, L.147, K.271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.271 GOL.74: 2 residues within 4Å: Chain C: D.291, A.292 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.292 GOL.96: 6 residues within 4Å: Chain D: K.271, G.272, F.273, N.274, L.275, E.276 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.272, D:N.274, D:E.276 Water bridges: D:N.274, D:L.275, D:L.275 GOL.97: 2 residues within 4Å: Chain D: D.291, A.292 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.292 Water bridges: D:D.291

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.26: 8 residues within 4Å: Chain A: N.67, T.79, F.82, I.169, L.192, G.193 Chain B: F.75 Ligands: CL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.67 Water bridges: A:I.169, A:I.169, A:K.171 EPE.75: 8 residues within 4Å: Chain C: N.67, T.79, F.82, I.169, L.192, G.193 Chain D: F.75 Ligands: CL.52 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.67 Water bridges: C:I.169, C:I.169, C:K.171

2 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.49: 11 residues within 4Å: Chain A: Q.61, Y.413, G.414, D.416, E.417 Chain B: W.57, Y.58, Y.413, G.414, D.416, E.417 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.58, B:Y.58, B:Y.413, B:Y.413, A:Q.61, A:Y.413 Water bridges: B:G.414, B:D.416, B:D.416, A:G.414, A:D.416 BDF.98: 11 residues within 4Å: Chain C: Q.61, Y.413, G.414, D.416, E.417 Chain D: W.57, Y.58, Y.413, G.414, D.416, E.417 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:Y.58, D:Y.413, C:Q.61, C:Y.413 Water bridges: D:K.54, D:Y.413, D:G.414, D:D.416, C:Y.413, C:G.414, C:D.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD. To Be Published

Release Date

2017-03-22

Peptides

Glutathione reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glutathione reductase

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