SMTL ID : 8rqz.1

Crystal structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

hetero-4-4-mer

Ligands

10 x MYR: MYRISTIC ACID(Non-covalent)

MYR.1: 9 residues within 4Å: Chain A: E.27, L.30 Chain F: E.27, L.30, T.40, L.44 Ligands: MYR.2, MYR.5, MYR.54 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:E.27, A:L.30, A:L.30, F:L.30, F:T.40, F:L.44 Hydrogen bonds: A:E.27 MYR.2: 8 residues within 4Å: Chain A: M.43, M.47, V.52 Chain F: L.56 Ligands: MYR.1, MYR.5, MYR.6, MYR.55 No protein-ligand interaction detected (PLIP) MYR.5: 10 residues within 4Å: Chain A: E.27, L.30, T.40, L.44 Chain B: E.27, L.30 Ligands: MYR.1, MYR.2, MYR.6, MYR.50 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.30, A:T.40, A:L.44, B:E.27, B:L.30, B:L.30 Hydrogen bonds: B:E.27 MYR.6: 8 residues within 4Å: Chain A: L.44, M.47, L.56 Chain B: M.43, M.47 Ligands: MYR.2, MYR.5, MYR.51 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.44, A:L.56 MYR.24: 13 residues within 4Å: Chain C: Y.98, V.101, D.103, G.213, E.214, T.219, G.220, I.221, N.222, N.223, L.226, R.227, I.230 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.98, C:L.226 Water bridges: C:E.96, C:Y.98, C:D.144 Salt bridges: C:K.134, C:R.227 MYR.50: 9 residues within 4Å: Chain B: E.27, L.30, T.40, L.44 Chain E: E.27, L.30 Ligands: MYR.5, MYR.51, MYR.54 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:L.30, B:T.40, B:L.44, E:E.27, E:L.30, E:L.30 Hydrogen bonds: E:E.27 MYR.51: 8 residues within 4Å: Chain B: L.56 Chain E: M.43, M.47, V.52 Ligands: MYR.6, MYR.50, MYR.54, MYR.55 No protein-ligand interaction detected (PLIP) MYR.54: 10 residues within 4Å: Chain E: E.27, L.30, T.40, L.44 Chain F: E.27, L.30 Ligands: MYR.1, MYR.50, MYR.51, MYR.55 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.30, E:T.40, E:L.44, F:E.27, F:L.30, F:L.30 Hydrogen bonds: F:E.27 MYR.55: 8 residues within 4Å: Chain E: L.44, M.47, L.56 Chain F: M.43, M.47 Ligands: MYR.2, MYR.51, MYR.54 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.44, E:L.56 MYR.73: 13 residues within 4Å: Chain G: Y.98, V.101, D.103, G.213, E.214, T.219, G.220, I.221, N.222, N.223, L.226, R.227, I.230 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:Y.98, G:L.226 Water bridges: G:E.96, G:Y.98, G:D.144 Salt bridges: G:K.134, G:R.227

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: L.38, H.42 Chain B: E.25 Chain F: R.57 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: R.57 Chain B: L.38, H.42 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: K.259, G.280, R.281, V.719, F.720, E.721 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain C: I.283, L.284, K.285, V.286, K.304, F.305, W.307, D.308 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain D: K.259, T.278, G.280, V.719, F.720, E.721 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain D: P.850, E.851, I.940, S.941, P.942 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain A: K.10 Chain D: E.313, R.315, L.316, T.317, K.318, E.329 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain D: I.283, V.286, K.304, F.305, W.307, D.308 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain B: R.57 Chain E: L.38, H.42 Chain F: E.25 Ligand excluded by PLIP GOL.53: 3 residues within 4Å: Chain E: R.57 Chain F: L.38, H.42 Ligand excluded by PLIP GOL.74: 6 residues within 4Å: Chain G: K.259, G.280, R.281, V.719, F.720, E.721 Ligand excluded by PLIP GOL.75: 8 residues within 4Å: Chain G: I.283, L.284, K.285, V.286, K.304, F.305, W.307, D.308 Ligand excluded by PLIP GOL.81: 6 residues within 4Å: Chain H: K.259, T.278, G.280, V.719, F.720, E.721 Ligand excluded by PLIP GOL.94: 5 residues within 4Å: Chain H: P.850, E.851, I.940, S.941, P.942 Ligand excluded by PLIP GOL.95: 7 residues within 4Å: Chain E: K.10 Chain H: E.313, R.315, L.316, T.317, K.318, E.329 Ligand excluded by PLIP GOL.96: 6 residues within 4Å: Chain H: I.283, V.286, K.304, F.305, W.307, D.308 Ligand excluded by PLIP

4 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.7: 15 residues within 4Å: Chain B: L.59, F.60, G.63, D.64, V.66, L.67 Chain D: Y.217, L.218, G.220, I.221 Chain E: E.49, R.50, G.51 Chain G: M.253 Ligands: MQ7.42 11 PLIP interactions: 2 interactions with chain E, 4 interactions with chain B, 5 interactions with chain D Hydrogen bonds: E:G.51, D:Y.217, D:G.220, D:I.221, D:N.222 Salt bridges: E:R.50 Hydrophobic interactions: B:L.59, B:F.60, B:V.66, B:L.67, D:L.218 LHG.20: 18 residues within 4Å: Chain C: Y.217, L.218, G.220, I.221, M.229, I.232, T.233 Chain D: I.246, M.249, M.253 Chain E: G.63, D.64, V.66, L.67, L.70 Chain F: E.49, R.50 Ligands: MQ7.16 9 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C, 1 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: D:I.246, C:L.218, C:I.232, E:L.67, E:L.70 Hydrogen bonds: C:G.220, C:I.221, E:L.67 Salt bridges: F:R.50 LHG.56: 15 residues within 4Å: Chain A: E.49, R.50, G.51 Chain C: M.253 Chain F: L.59, F.60, G.63, D.64, V.66, L.67 Chain H: Y.217, L.218, G.220, I.221 Ligands: MQ7.91 11 PLIP interactions: 5 interactions with chain H, 4 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: H:L.218, F:L.59, F:F.60, F:V.66, F:L.67 Hydrogen bonds: H:Y.217, H:G.220, H:I.221, H:N.222, A:G.51 Salt bridges: A:R.50 LHG.69: 18 residues within 4Å: Chain A: G.63, D.64, V.66, L.67, L.70 Chain B: E.49, R.50 Chain G: Y.217, L.218, G.220, I.221, M.229, I.232, T.233 Chain H: I.246, M.249, M.253 Ligands: MQ7.65 9 PLIP interactions: 3 interactions with chain A, 4 interactions with chain G, 1 interactions with chain H, 1 interactions with chain B Hydrophobic interactions: A:L.67, A:L.70, G:L.218, G:I.232, H:I.246 Hydrogen bonds: A:L.67, G:G.220, G:I.221 Salt bridges: B:R.50

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.8: 10 residues within 4Å: Chain C: Q.35, C.37, Y.38, E.46, C.48, D.49, T.50, C.51, R.61, C.63 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.37, C:C.48, C:C.51, C:C.63 FES.34: 10 residues within 4Å: Chain D: Q.35, C.37, Y.38, E.46, T.47, C.48, D.49, C.51, R.61, C.63 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.37, D:C.48, D:C.51, D:C.63 FES.57: 10 residues within 4Å: Chain G: Q.35, C.37, Y.38, E.46, C.48, D.49, T.50, C.51, R.61, C.63 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.37, G:C.48, G:C.51, G:C.63 FES.83: 10 residues within 4Å: Chain H: Q.35, C.37, Y.38, E.46, T.47, C.48, D.49, C.51, R.61, C.63 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.37, H:C.48, H:C.51, H:C.63

16 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.9: 14 residues within 4Å: Chain C: H.95, E.96, L.97, Y.98, C.99, C.102, Y.104, N.105, C.109, I.111, H.112, Q.147, C.203, N.204 5 PLIP interactions: 5 interactions with chain C, pi-Cation interactions: C:Y.98 Metal complexes: C:H.95, C:C.99, C:C.102, C:C.109 SF4.10: 14 residues within 4Å: Chain C: Y.143, C.148, I.149, L.150, C.151, G.152, R.153, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.148, C:C.151, C:C.154, C:C.201 SF4.11: 12 residues within 4Å: Chain C: Y.141, C.158, T.164, L.167, W.180, C.191, V.192, S.193, C.194, G.195, H.196, C.197 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.158, C:C.191, C:C.194, C:C.197 SF4.12: 11 residues within 4Å: Chain C: C.265, Y.267, C.268, V.270, G.271, C.272, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.265, C:C.268, C:C.272, C:C.300 SF4.35: 13 residues within 4Å: Chain D: H.95, E.96, L.97, Y.98, C.99, C.102, Y.104, N.105, C.109, I.111, H.112, C.203, N.204 5 PLIP interactions: 5 interactions with chain D, pi-Cation interactions: D:Y.98 Metal complexes: D:H.95, D:C.99, D:C.102, D:C.109 SF4.36: 14 residues within 4Å: Chain D: Y.143, C.148, I.149, L.150, C.151, G.152, R.153, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.148, D:C.151, D:C.154, D:C.201 SF4.37: 12 residues within 4Å: Chain D: Y.141, C.158, T.164, L.167, W.180, C.191, V.192, S.193, C.194, G.195, H.196, C.197 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.158, D:C.191, D:C.194, D:C.197 SF4.38: 11 residues within 4Å: Chain D: C.265, Y.267, C.268, V.270, G.271, C.272, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.265, D:C.268, D:C.272, D:C.300 SF4.58: 14 residues within 4Å: Chain G: H.95, E.96, L.97, Y.98, C.99, C.102, Y.104, N.105, C.109, I.111, H.112, Q.147, C.203, N.204 5 PLIP interactions: 5 interactions with chain G, pi-Cation interactions: G:Y.98 Metal complexes: G:H.95, G:C.99, G:C.102, G:C.109 SF4.59: 14 residues within 4Å: Chain G: Y.143, C.148, I.149, L.150, C.151, G.152, R.153, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.148, G:C.151, G:C.154, G:C.201 SF4.60: 12 residues within 4Å: Chain G: Y.141, C.158, T.164, L.167, W.180, C.191, V.192, S.193, C.194, G.195, H.196, C.197 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.158, G:C.191, G:C.194, G:C.197 SF4.61: 11 residues within 4Å: Chain G: C.265, Y.267, C.268, V.270, G.271, C.272, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.265, G:C.268, G:C.272, G:C.300 SF4.84: 13 residues within 4Å: Chain H: H.95, E.96, L.97, Y.98, C.99, C.102, Y.104, N.105, C.109, I.111, H.112, C.203, N.204 5 PLIP interactions: 5 interactions with chain H, pi-Cation interactions: H:Y.98 Metal complexes: H:H.95, H:C.99, H:C.102, H:C.109 SF4.85: 14 residues within 4Å: Chain H: Y.143, C.148, I.149, L.150, C.151, G.152, R.153, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.148, H:C.151, H:C.154, H:C.201 SF4.86: 12 residues within 4Å: Chain H: Y.141, C.158, T.164, L.167, W.180, C.191, V.192, S.193, C.194, G.195, H.196, C.197 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.158, H:C.191, H:C.194, H:C.197 SF4.87: 11 residues within 4Å: Chain H: C.265, Y.267, C.268, V.270, G.271, C.272, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.265, H:C.268, H:C.272, H:C.300

8 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.13: 38 residues within 4Å: Chain C: K.362, C.363, C.387, Y.390, C.391, Q.553, H.587, G.653, E.654, E.655, V.659, Q.679, D.680, I.681, F.682, S.684, A.696, S.697, P.698, S.699, K.702, D.729, N.826, R.828, F.833, H.834, E.835, N.837, L.838, M.900, I.908, N.909, T.912, Y.925, K.926 Ligands: MGD.14, 4MO.15, H2S.17 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:Q.553, C:G.653, C:E.655, C:V.659, C:Q.679, C:I.681, C:S.699, C:K.702, C:K.702, C:N.826, C:R.828, C:R.828, C:N.837, C:N.909, C:N.909, C:K.926 Water bridges: C:T.266, C:N.837 Salt bridges: C:H.587, C:H.587, C:D.680, C:D.729, C:H.834, C:H.834 pi-Stacking: C:Y.925 pi-Cation interactions: C:Y.925 MGD.14: 37 residues within 4Å: Chain C: C.268, K.302, C.391, I.424, G.425, S.426, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.13, 4MO.15, H2S.17 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:K.302, C:G.425, C:N.427, C:S.431, C:S.431, C:A.453, C:I.455, C:R.456, C:G.473, C:M.549, C:N.825, C:R.828, C:R.828, C:L.829, C:H.832, C:H.834, C:H.834 Water bridges: C:N.427, C:R.456, C:R.456, C:R.456, C:L.829 Salt bridges: C:D.454, C:D.475, C:R.828, C:K.926 MGD.39: 38 residues within 4Å: Chain D: K.362, C.363, C.387, Y.390, C.391, Q.553, H.587, G.653, E.654, E.655, V.659, Q.679, D.680, I.681, F.682, S.684, A.696, S.697, P.698, S.699, K.702, D.729, N.826, R.828, F.833, H.834, E.835, N.837, L.838, M.900, I.908, N.909, T.912, Y.925, K.926 Ligands: MGD.40, 4MO.41, H2S.43 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:Q.553, D:G.653, D:E.655, D:V.659, D:Q.679, D:I.681, D:S.699, D:K.702, D:K.702, D:N.826, D:R.828, D:R.828, D:N.837, D:N.909, D:N.909, D:K.926, D:K.926 Water bridges: D:N.837 Salt bridges: D:H.587, D:H.587, D:D.680, D:D.729, D:H.834, D:H.834 pi-Stacking: D:Y.925 pi-Cation interactions: D:Y.925 MGD.40: 37 residues within 4Å: Chain D: C.268, K.302, C.391, I.424, G.425, S.426, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.39, 4MO.41, H2S.43 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:K.302, D:G.425, D:N.427, D:S.431, D:S.431, D:S.431, D:A.453, D:I.455, D:R.456, D:H.458, D:G.473, D:M.549, D:N.825, D:R.828, D:L.829, D:H.832, D:H.834, D:H.834 Water bridges: D:N.427, D:H.432 Salt bridges: D:D.454, D:D.475, D:R.828, D:R.828, D:K.926 MGD.62: 38 residues within 4Å: Chain G: K.362, C.363, C.387, Y.390, C.391, Q.553, H.587, G.653, E.654, E.655, V.659, Q.679, D.680, I.681, F.682, S.684, A.696, S.697, P.698, S.699, K.702, D.729, N.826, R.828, F.833, H.834, E.835, N.837, L.838, M.900, I.908, N.909, T.912, Y.925, K.926 Ligands: MGD.63, 4MO.64, H2S.66 26 PLIP interactions: 26 interactions with chain G Hydrogen bonds: G:Q.553, G:G.653, G:E.655, G:V.659, G:Q.679, G:I.681, G:S.699, G:K.702, G:K.702, G:N.826, G:R.828, G:R.828, G:N.837, G:N.909, G:N.909, G:K.926 Water bridges: G:T.266, G:N.837 Salt bridges: G:H.587, G:H.587, G:D.680, G:D.729, G:H.834, G:H.834 pi-Stacking: G:Y.925 pi-Cation interactions: G:Y.925 MGD.63: 37 residues within 4Å: Chain G: C.268, K.302, C.391, I.424, G.425, S.426, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.62, 4MO.64, H2S.66 26 PLIP interactions: 26 interactions with chain G Hydrogen bonds: G:K.302, G:G.425, G:N.427, G:S.431, G:S.431, G:A.453, G:I.455, G:R.456, G:G.473, G:M.549, G:N.825, G:R.828, G:R.828, G:L.829, G:H.832, G:H.834, G:H.834 Water bridges: G:N.427, G:R.456, G:R.456, G:R.456, G:L.829 Salt bridges: G:D.454, G:D.475, G:R.828, G:K.926 MGD.88: 38 residues within 4Å: Chain H: K.362, C.363, C.387, Y.390, C.391, Q.553, H.587, G.653, E.654, E.655, V.659, Q.679, D.680, I.681, F.682, S.684, A.696, S.697, P.698, S.699, K.702, D.729, N.826, R.828, F.833, H.834, E.835, N.837, L.838, M.900, I.908, N.909, T.912, Y.925, K.926 Ligands: MGD.89, 4MO.90, H2S.92 26 PLIP interactions: 26 interactions with chain H Hydrogen bonds: H:Q.553, H:G.653, H:E.655, H:V.659, H:Q.679, H:I.681, H:S.699, H:K.702, H:K.702, H:N.826, H:R.828, H:R.828, H:N.837, H:N.909, H:N.909, H:K.926, H:K.926 Water bridges: H:N.837 Salt bridges: H:H.587, H:H.587, H:D.680, H:D.729, H:H.834, H:H.834 pi-Stacking: H:Y.925 pi-Cation interactions: H:Y.925 MGD.89: 37 residues within 4Å: Chain H: C.268, K.302, C.391, I.424, G.425, S.426, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.88, 4MO.90, H2S.92 25 PLIP interactions: 25 interactions with chain H Hydrogen bonds: H:K.302, H:G.425, H:N.427, H:S.431, H:S.431, H:S.431, H:A.453, H:I.455, H:R.456, H:H.458, H:G.473, H:M.549, H:N.825, H:R.828, H:L.829, H:H.832, H:H.834, H:H.834 Water bridges: H:N.427, H:H.432 Salt bridges: H:D.454, H:D.475, H:R.828, H:R.828, H:K.926

4 x 4MO: MOLYBDENUM(IV) ION(Non-covalent)

4MO.15: 5 residues within 4Å: Chain C: C.391, G.586 Ligands: MGD.13, MGD.14, H2S.17 No protein-ligand interaction detected (PLIP) 4MO.41: 5 residues within 4Å: Chain D: C.391, R.828 Ligands: MGD.39, MGD.40, H2S.43 No protein-ligand interaction detected (PLIP) 4MO.64: 5 residues within 4Å: Chain G: C.391, G.586 Ligands: MGD.62, MGD.63, H2S.66 No protein-ligand interaction detected (PLIP) 4MO.90: 5 residues within 4Å: Chain H: C.391, R.828 Ligands: MGD.88, MGD.89, H2S.92 No protein-ligand interaction detected (PLIP)

4 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.16: 14 residues within 4Å: Chain C: L.97, Y.98, C.99, T.100, V.101, M.229, I.230, T.233, K.234, E.237, Y.240, I.243, L.244 Ligands: LHG.20 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.97, C:V.101, C:I.230, C:T.233, C:T.233, C:K.234, C:Y.240, C:Y.240, C:I.243, C:I.243, C:L.244 Hydrogen bonds: C:T.100, C:T.100 MQ7.42: 16 residues within 4Å: Chain D: L.97, Y.98, C.99, T.100, V.101, L.218, M.229, I.230, T.233, K.234, E.237, Y.240, I.243, L.244, I.246 Ligands: LHG.7 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.97, D:T.100, D:V.101, D:L.218, D:I.230, D:T.233, D:T.233, D:Y.240, D:Y.240, D:I.243, D:I.243, D:L.244, D:I.246 Hydrogen bonds: D:T.100, D:T.100 MQ7.65: 14 residues within 4Å: Chain G: L.97, Y.98, C.99, T.100, V.101, M.229, I.230, T.233, K.234, E.237, Y.240, I.243, L.244 Ligands: LHG.69 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:L.97, G:V.101, G:I.230, G:T.233, G:T.233, G:K.234, G:Y.240, G:Y.240, G:I.243, G:I.243, G:L.244 Hydrogen bonds: G:T.100, G:T.100 MQ7.91: 16 residues within 4Å: Chain H: L.97, Y.98, C.99, T.100, V.101, L.218, M.229, I.230, T.233, K.234, E.237, Y.240, I.243, L.244, I.246 Ligands: LHG.56 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:L.97, H:T.100, H:V.101, H:L.218, H:I.230, H:T.233, H:T.233, H:Y.240, H:Y.240, H:I.243, H:I.243, H:L.244, H:I.246 Hydrogen bonds: H:T.100, H:T.100

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.17: 9 residues within 4Å: Chain C: C.387, C.391, Q.392, G.586, H.587, V.590 Ligands: MGD.13, MGD.14, 4MO.15 No protein-ligand interaction detected (PLIP) H2S.43: 8 residues within 4Å: Chain D: C.387, C.391, G.586, H.587, V.590 Ligands: MGD.39, MGD.40, 4MO.41 No protein-ligand interaction detected (PLIP) H2S.66: 9 residues within 4Å: Chain G: C.387, C.391, Q.392, G.586, H.587, V.590 Ligands: MGD.62, MGD.63, 4MO.64 No protein-ligand interaction detected (PLIP) H2S.92: 8 residues within 4Å: Chain H: C.387, C.391, G.586, H.587, V.590 Ligands: MGD.88, MGD.89, 4MO.90 No protein-ligand interaction detected (PLIP)

18 x MLI: MALONATE ION(Non-functional Binders)

MLI.18: 5 residues within 4Å: Chain C: Y.840, P.850, E.851, D.902, S.903 Ligand excluded by PLIP MLI.19: 5 residues within 4Å: Chain C: N.106, G.107, S.251, D.255, K.260 Ligand excluded by PLIP MLI.22: 4 residues within 4Å: Chain C: N.121, T.238, G.239, S.242 Ligand excluded by PLIP MLI.27: 6 residues within 4Å: Chain C: R.389, P.600, D.601, G.631, T.633, D.919 Ligand excluded by PLIP MLI.28: 9 residues within 4Å: Chain B: I.8, K.10 Chain C: E.313, E.314, R.315, L.316, T.317, K.318, E.329 Ligand excluded by PLIP MLI.29: 6 residues within 4Å: Chain C: Y.405, S.788, L.790, L.791, F.792, T.793 Ligand excluded by PLIP MLI.31: 5 residues within 4Å: Chain D: L.42, G.43, P.44, E.156, D.160 Ligand excluded by PLIP MLI.44: 6 residues within 4Å: Chain D: E.835, Y.840, P.850, E.851, D.902, S.903 Ligand excluded by PLIP MLI.48: 7 residues within 4Å: Chain D: Y.405, S.788, L.790, L.791, F.792, T.793, R.795 Ligand excluded by PLIP MLI.67: 5 residues within 4Å: Chain G: Y.840, P.850, E.851, D.902, S.903 Ligand excluded by PLIP MLI.68: 5 residues within 4Å: Chain G: N.106, G.107, S.251, D.255, K.260 Ligand excluded by PLIP MLI.71: 4 residues within 4Å: Chain G: N.121, T.238, G.239, S.242 Ligand excluded by PLIP MLI.76: 6 residues within 4Å: Chain G: R.389, P.600, D.601, G.631, T.633, D.919 Ligand excluded by PLIP MLI.77: 9 residues within 4Å: Chain F: I.8, K.10 Chain G: E.313, E.314, R.315, L.316, T.317, K.318, E.329 Ligand excluded by PLIP MLI.78: 6 residues within 4Å: Chain G: Y.405, S.788, L.790, L.791, F.792, T.793 Ligand excluded by PLIP MLI.80: 5 residues within 4Å: Chain H: L.42, G.43, P.44, E.156, D.160 Ligand excluded by PLIP MLI.93: 6 residues within 4Å: Chain H: E.835, Y.840, P.850, E.851, D.902, S.903 Ligand excluded by PLIP MLI.97: 7 residues within 4Å: Chain H: Y.405, S.788, L.790, L.791, F.792, T.793, R.795 Ligand excluded by PLIP

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.21: 8 residues within 4Å: Chain C: L.658, I.663, H.667, R.685, S.903, G.904, A.907, L.910 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.685, C:R.685, C:G.904 NO3.23: 6 residues within 4Å: Chain C: R.376, G.377, I.379, G.380, V.624, P.625 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.378, C:P.625 NO3.30: 8 residues within 4Å: Chain D: L.658, I.663, H.667, R.685, S.903, G.904, A.907, L.910 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.685, D:S.903 NO3.33: 4 residues within 4Å: Chain D: N.106, S.251, D.255, K.260 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.251, D:K.260, D:K.260 NO3.70: 8 residues within 4Å: Chain G: L.658, I.663, H.667, R.685, S.903, G.904, A.907, L.910 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.685, G:R.685, G:G.904 NO3.72: 6 residues within 4Å: Chain G: R.376, G.377, I.379, G.380, V.624, P.625 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:V.378, G:P.625 NO3.79: 8 residues within 4Å: Chain H: L.658, I.663, H.667, R.685, S.903, G.904, A.907, L.910 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.685, H:S.903 NO3.82: 4 residues within 4Å: Chain H: N.106, S.251, D.255, K.260 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.251, H:K.260, H:K.260

2 x NA: SODIUM ION(Non-functional Binders)

NA.49: 4 residues within 4Å: Chain D: Y.104, S.198, T.199, C.201 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.201 NA.98: 4 residues within 4Å: Chain H: Y.104, S.198, T.199, C.201 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:C.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherrier, M.V. et al., Conserved Helical Membrane Plug-in for Quinone reductases. To Be Published

Release Date

2025-08-06

Peptides

Uncharacterized protein YjgD: ABEF
Probable oxidoreductase YjgC: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

C
C

D
D

G
C

H
D

Uncharacterized protein YjgD

Probable oxidoreductase YjgC

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