SMTL ID : 8rr0.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

24 x 11A: UNDECANOIC ACID(Non-covalent)(Non-functional Binders)

11A.1: 9 residues within 4Å: Chain A: L.23, I.26, E.27 Chain C: L.30, I.37, T.40, L.41 Ligands: 11A.26, 11A.72 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.30, C:I.37, C:T.40, C:L.41 Hydrogen bonds: A:E.27 11A.6: 3 residues within 4Å: Chain A: L.134, N.140 Chain C: F.128 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.128 Hydrogen bonds: C:F.128, C:F.128 11A.7: 2 residues within 4Å: Chain A: F.128 Ligands: 11A.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.128 11A.9: 3 residues within 4Å: Chain A: Q.118, K.119 Ligands: 11A.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.119 11A.10: 4 residues within 4Å: Ligands: 01.3, 01.28, 11A.35, 11A.81 No protein-ligand interaction detected (PLIP) 11A.11: 7 residues within 4Å: Chain A: G.154, Q.155, D.156 Chain C: P.103, K.107, K.141 Chain E: K.119 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:K.119 Hydrophobic interactions: C:K.141, C:K.141 11A.26: 9 residues within 4Å: Chain C: L.23, I.26, E.27 Chain E: L.30, I.37, T.40, L.41 Ligands: 11A.1, 11A.49 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:L.30, E:I.37, E:T.40, E:L.41 Hydrogen bonds: C:E.27 11A.31: 3 residues within 4Å: Chain C: L.134, N.140 Chain E: F.128 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.128 Hydrogen bonds: E:F.128, E:F.128 11A.32: 2 residues within 4Å: Chain C: F.128 Ligands: 11A.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.128 11A.34: 3 residues within 4Å: Chain C: Q.118, K.119 Ligands: 11A.32 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.119 11A.35: 4 residues within 4Å: Ligands: 11A.10, 01.28, 01.51, 11A.58 No protein-ligand interaction detected (PLIP) 11A.36: 7 residues within 4Å: Chain C: G.154, Q.155, D.156 Chain E: P.103, K.107, K.141 Chain G: K.119 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: E:K.141, E:K.141 Hydrogen bonds: G:K.119 11A.49: 9 residues within 4Å: Chain E: L.23, I.26, E.27 Chain G: L.30, I.37, T.40, L.41 Ligands: 11A.26, 11A.72 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain G Hydrogen bonds: E:E.27 Hydrophobic interactions: G:L.30, G:I.37, G:T.40, G:L.41 11A.54: 3 residues within 4Å: Chain E: L.134, N.140 Chain G: F.128 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:F.128 Hydrogen bonds: G:F.128, G:F.128 11A.55: 2 residues within 4Å: Chain E: F.128 Ligands: 11A.57 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.128 11A.57: 3 residues within 4Å: Chain E: Q.118, K.119 Ligands: 11A.55 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.119 11A.58: 4 residues within 4Å: Ligands: 11A.35, 01.51, 01.74, 11A.81 No protein-ligand interaction detected (PLIP) 11A.59: 7 residues within 4Å: Chain A: K.119 Chain E: G.154, Q.155, D.156 Chain G: P.103, K.107, K.141 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:K.141, G:K.141 Hydrogen bonds: A:K.119 11A.72: 9 residues within 4Å: Chain A: L.30, I.37, T.40, L.41 Chain G: L.23, I.26, E.27 Ligands: 11A.1, 11A.49 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:L.30, A:I.37, A:T.40, A:L.41 Hydrogen bonds: G:E.27 11A.77: 3 residues within 4Å: Chain A: F.128 Chain G: L.134, N.140 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.128 Hydrogen bonds: A:F.128, A:F.128 11A.78: 2 residues within 4Å: Chain G: F.128 Ligands: 11A.80 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.128 11A.80: 3 residues within 4Å: Chain G: Q.118, K.119 Ligands: 11A.78 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.119 11A.81: 4 residues within 4Å: Ligands: 01.3, 11A.10, 11A.58, 01.74 No protein-ligand interaction detected (PLIP) 11A.82: 7 residues within 4Å: Chain A: P.103, K.107, K.141 Chain C: K.119 Chain G: G.154, Q.155, D.156 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:K.141, A:K.141 Hydrogen bonds: C:K.119

12 x 01: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate

01.2: 14 residues within 4Å: Chain A: L.70, K.73, E.78, T.79 Chain C: L.87 Chain H: I.232, V.236, T.238, S.242, I.246 Ligands: 01.27, MQ7.69, 01.73, MQ7.92 10 PLIP interactions: 3 interactions with chain H, 2 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: H:I.232, H:V.236, H:I.246, C:L.87, C:L.87, A:L.70, A:K.73, A:T.79 Hydrogen bonds: A:K.73, A:K.73 01.3: 11 residues within 4Å: Chain A: I.130, I.131, L.134 Chain E: F.147 Ligands: SHV.4, SHV.5, 11A.10, 01.28, 01.51, 01.74, 11A.81 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.130, A:I.131, A:I.131, A:L.134 01.13: 21 residues within 4Å: Chain A: E.49, R.50, V.52, L.55 Chain B: I.246, E.250 Chain C: L.55, L.59, G.63, D.64, V.66, L.67 Chain H: Y.217, L.218, G.220, I.221, N.222 Ligands: MYR.24, 01.25, 01.71, MQ7.92 11 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A, 2 interactions with chain H, 4 interactions with chain C Hydrophobic interactions: B:I.246, A:V.52, A:L.55, C:L.55, C:L.59, C:V.66, C:L.67 Hydrogen bonds: A:R.50, H:N.222, H:N.222 Salt bridges: A:R.50 01.25: 21 residues within 4Å: Chain B: Y.217, L.218, G.220, I.221, N.222 Chain C: E.49, R.50, V.52, L.55 Chain D: I.246, E.250 Chain E: L.55, L.59, G.63, D.64, V.66, L.67 Ligands: 01.13, MQ7.23, MYR.47, 01.48 11 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B, 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: C:V.52, C:L.55, E:L.55, E:L.59, E:V.66, E:L.67, D:I.246 Hydrogen bonds: C:R.50, B:N.222, B:N.222 Salt bridges: C:R.50 01.27: 14 residues within 4Å: Chain B: I.232, V.236, T.238, S.242, I.246 Chain C: L.70, K.73, E.78, T.79 Chain E: L.87 Ligands: 01.2, MQ7.23, 01.50, MQ7.92 10 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: B:I.232, B:V.236, B:I.246, C:L.70, C:K.73, C:T.79, E:L.87, E:L.87 Hydrogen bonds: C:K.73, C:K.73 01.28: 11 residues within 4Å: Chain C: I.130, I.131, L.134 Chain G: F.147 Ligands: 01.3, 11A.10, SHV.29, SHV.30, 11A.35, 01.51, 01.74 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.130, C:I.131, C:I.131, C:L.134 01.48: 21 residues within 4Å: Chain D: Y.217, L.218, G.220, I.221, N.222 Chain E: E.49, R.50, V.52, L.55 Chain F: I.246, E.250 Chain G: L.55, L.59, G.63, D.64, V.66, L.67 Ligands: 01.25, MQ7.46, MYR.70, 01.71 11 PLIP interactions: 4 interactions with chain E, 4 interactions with chain G, 2 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: E:V.52, E:L.55, G:L.55, G:L.59, G:V.66, G:L.67, F:I.246 Hydrogen bonds: E:R.50, D:N.222, D:N.222 Salt bridges: E:R.50 01.50: 14 residues within 4Å: Chain D: I.232, V.236, T.238, S.242, I.246 Chain E: L.70, K.73, E.78, T.79 Chain G: L.87 Ligands: MQ7.23, 01.27, MQ7.46, 01.73 10 PLIP interactions: 3 interactions with chain D, 5 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: D:I.232, D:V.236, D:I.246, E:L.70, E:K.73, E:T.79, G:L.87, G:L.87 Hydrogen bonds: E:K.73, E:K.73 01.51: 11 residues within 4Å: Chain A: F.147 Chain E: I.130, I.131, L.134 Ligands: 01.3, 01.28, 11A.35, SHV.52, SHV.53, 11A.58, 01.74 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.130, E:I.131, E:I.131, E:L.134 01.71: 21 residues within 4Å: Chain A: L.55, L.59, G.63, D.64, V.66, L.67 Chain F: Y.217, L.218, G.220, I.221, N.222 Chain G: E.49, R.50, V.52, L.55 Chain H: I.246, E.250 Ligands: MYR.12, 01.13, 01.48, MQ7.69 11 PLIP interactions: 4 interactions with chain G, 4 interactions with chain A, 1 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: G:V.52, G:L.55, A:L.55, A:L.59, A:V.66, A:L.67, H:I.246 Hydrogen bonds: G:R.50, F:N.222, F:N.222 Salt bridges: G:R.50 01.73: 14 residues within 4Å: Chain A: L.87 Chain F: I.232, V.236, T.238, S.242, I.246 Chain G: L.70, K.73, E.78, T.79 Ligands: 01.2, MQ7.46, 01.50, MQ7.69 10 PLIP interactions: 5 interactions with chain G, 3 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: G:L.70, G:K.73, G:T.79, F:I.232, F:V.236, F:I.246, A:L.87, A:L.87 Hydrogen bonds: G:K.73, G:K.73 01.74: 11 residues within 4Å: Chain C: F.147 Chain G: I.130, I.131, L.134 Ligands: 01.3, 01.28, 01.51, 11A.58, SHV.75, SHV.76, 11A.81 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:I.130, G:I.131, G:I.131, G:L.134

8 x SHV: HEPTANOIC ACID(Non-covalent)

SHV.4: 2 residues within 4Å: Chain A: I.131 Ligands: 01.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.135 SHV.5: 2 residues within 4Å: Chain A: I.131 Ligands: 01.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.132 SHV.29: 2 residues within 4Å: Chain C: I.131 Ligands: 01.28 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.135 SHV.30: 2 residues within 4Å: Chain C: I.131 Ligands: 01.28 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.132 SHV.52: 2 residues within 4Å: Chain E: I.131 Ligands: 01.51 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.135 SHV.53: 2 residues within 4Å: Chain E: I.131 Ligands: 01.51 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.132 SHV.75: 2 residues within 4Å: Chain G: I.131 Ligands: 01.74 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.135 SHV.76: 2 residues within 4Å: Chain G: I.131 Ligands: 01.74 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.132

4 x KNA: nonanoic acid(Non-covalent)

KNA.8: 2 residues within 4Å: Chain A: R.132, K.135 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.135 KNA.33: 2 residues within 4Å: Chain C: R.132, K.135 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.135 KNA.56: 2 residues within 4Å: Chain E: R.132, K.135 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.135 KNA.79: 2 residues within 4Å: Chain G: R.132, K.135 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.135

4 x MYR: MYRISTIC ACID(Non-covalent)

MYR.12: 7 residues within 4Å: Chain A: L.44, M.47, L.56, F.60 Ligands: MYR.24, MYR.70, 01.71 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.44, A:L.56, A:F.60 MYR.24: 7 residues within 4Å: Chain C: L.44, M.47, L.56, F.60 Ligands: MYR.12, 01.13, MYR.47 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.44, C:L.56, C:F.60 MYR.47: 7 residues within 4Å: Chain E: L.44, M.47, L.56, F.60 Ligands: MYR.24, 01.25, MYR.70 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.44, E:L.56, E:F.60 MYR.70: 7 residues within 4Å: Chain G: L.44, M.47, L.56, F.60 Ligands: MYR.12, MYR.47, 01.48 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.44, G:L.56, G:F.60

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

FES.14: 9 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.37, B:C.48, B:C.51, B:C.63 FES.37: 9 residues within 4Å: Chain D: 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.60: 9 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.37, F:C.48, F:C.51, F:C.63 FES.83: 9 residues within 4Å: Chain H: 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)

SF4.15: 12 residues within 4Å: Chain B: H.95, L.97, Y.98, C.99, C.102, N.105, C.109, I.111, H.112, Q.147, C.203, N.204 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:Y.98 Metal complexes: B:H.95, B:C.99, B:C.102, B:C.109 SF4.16: 13 residues within 4Å: Chain B: Y.143, C.148, I.149, L.150, C.151, G.152, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.148, B:C.151, B:C.154, B:C.201 SF4.17: 12 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.158, B:C.191, B:C.194, B:C.197 SF4.18: 12 residues within 4Å: Chain B: C.265, Y.267, C.268, G.271, C.272, F.274, T.299, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.265, B:C.268, B:C.272, B:C.300 SF4.38: 12 residues within 4Å: Chain D: H.95, L.97, Y.98, C.99, C.102, N.105, C.109, I.111, H.112, Q.147, 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 SF4.39: 13 residues within 4Å: Chain D: Y.143, C.148, I.149, L.150, C.151, G.152, 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 SF4.40: 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 SF4.41: 12 residues within 4Å: Chain D: C.265, Y.267, C.268, G.271, C.272, F.274, T.299, 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 SF4.61: 12 residues within 4Å: Chain F: H.95, L.97, Y.98, C.99, C.102, N.105, C.109, I.111, H.112, Q.147, C.203, N.204 5 PLIP interactions: 5 interactions with chain F, pi-Cation interactions: F:Y.98 Metal complexes: F:H.95, F:C.99, F:C.102, F:C.109 SF4.62: 13 residues within 4Å: Chain F: Y.143, C.148, I.149, L.150, C.151, G.152, C.154, V.178, C.201, P.202, C.203, A.205, M.206 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.148, F:C.151, F:C.154, F:C.201 SF4.63: 12 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.158, F:C.191, F:C.194, F:C.197 SF4.64: 12 residues within 4Å: Chain F: C.265, Y.267, C.268, G.271, C.272, F.274, T.299, C.300, K.302, G.303, P.433, V.434 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.265, F:C.268, F:C.272, F:C.300 SF4.84: 12 residues within 4Å: Chain H: H.95, L.97, Y.98, C.99, C.102, N.105, C.109, I.111, H.112, Q.147, 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: 13 residues within 4Å: Chain H: Y.143, C.148, I.149, L.150, C.151, G.152, 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: 12 residues within 4Å: Chain H: C.265, Y.267, C.268, G.271, C.272, F.274, T.299, 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.19: 37 residues within 4Å: Chain B: 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, Y.925, K.926 Ligands: MGD.20, 4MO.21, H2S.22 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:K.362, B:Q.553, B:E.655, B:E.655, B:E.655, B:E.655, B:V.659, B:Q.679, B:F.682, B:S.699, B:K.702, B:K.702, B:N.826, B:N.826, B:R.828, B:R.828, B:E.835, B:N.837, B:N.909, B:N.909, B:K.926 Salt bridges: B:K.362, B:H.587, B:H.587, B:D.729, B:H.834, B:H.834 pi-Stacking: B:Y.925 MGD.20: 39 residues within 4Å: Chain B: C.268, K.302, C.391, Q.392, I.424, G.425, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, R.471, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, N.826, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.19, 4MO.21, H2S.22 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:K.302, B:G.425, B:N.427, B:N.427, B:S.431, B:S.431, B:A.453, B:I.455, B:R.456, B:G.473, B:M.549, B:G.550, B:N.825, B:R.828, B:R.828, B:H.832, B:H.832, B:H.834, B:H.834, B:Y.897 Salt bridges: B:H.432, B:D.475, B:R.828, B:R.828, B:K.926 pi-Stacking: B:H.834 MGD.42: 37 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, Y.925, K.926 Ligands: MGD.43, 4MO.44, H2S.45 28 PLIP interactions: 28 interactions with chain D Hydrogen bonds: D:K.362, D:Q.553, D:E.655, D:E.655, D:E.655, D:E.655, D:V.659, D:Q.679, D:F.682, D:S.699, D:K.702, D:K.702, D:N.826, D:N.826, D:R.828, D:R.828, D:E.835, D:N.837, D:N.909, D:N.909, D:K.926 Salt bridges: D:K.362, D:H.587, D:H.587, D:D.729, D:H.834, D:H.834 pi-Stacking: D:Y.925 MGD.43: 39 residues within 4Å: Chain D: C.268, K.302, C.391, Q.392, I.424, G.425, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, R.471, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, N.826, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.42, 4MO.44, H2S.45 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:K.302, D:G.425, D:N.427, D:N.427, D:S.431, D:S.431, D:A.453, D:I.455, D:R.456, D:G.473, D:M.549, D:G.550, D:N.825, D:R.828, D:R.828, D:H.832, D:H.832, D:H.834, D:H.834, D:Y.897 Salt bridges: D:H.432, D:D.475, D:R.828, D:R.828, D:K.926 pi-Stacking: D:H.834 MGD.65: 37 residues within 4Å: Chain F: 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, Y.925, K.926 Ligands: MGD.66, 4MO.67, H2S.68 28 PLIP interactions: 28 interactions with chain F Hydrogen bonds: F:K.362, F:Q.553, F:E.655, F:E.655, F:E.655, F:E.655, F:V.659, F:Q.679, F:F.682, F:S.699, F:K.702, F:K.702, F:N.826, F:N.826, F:R.828, F:R.828, F:E.835, F:N.837, F:N.909, F:N.909, F:K.926 Salt bridges: F:K.362, F:H.587, F:H.587, F:D.729, F:H.834, F:H.834 pi-Stacking: F:Y.925 MGD.66: 39 residues within 4Å: Chain F: C.268, K.302, C.391, Q.392, I.424, G.425, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, R.471, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, N.826, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.65, 4MO.67, H2S.68 26 PLIP interactions: 26 interactions with chain F Hydrogen bonds: F:K.302, F:G.425, F:N.427, F:N.427, F:S.431, F:S.431, F:A.453, F:I.455, F:R.456, F:G.473, F:M.549, F:G.550, F:N.825, F:R.828, F:R.828, F:H.832, F:H.832, F:H.834, F:H.834, F:Y.897 Salt bridges: F:H.432, F:D.475, F:R.828, F:R.828, F:K.926 pi-Stacking: F:H.834 MGD.88: 37 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, Y.925, K.926 Ligands: MGD.89, 4MO.90, H2S.91 28 PLIP interactions: 28 interactions with chain H Hydrogen bonds: H:K.362, H:Q.553, H:E.655, H:E.655, H:E.655, H:E.655, H:V.659, H:Q.679, H:F.682, H:S.699, H:K.702, H:K.702, H:N.826, H:N.826, H:R.828, H:R.828, H:E.835, H:N.837, H:N.909, H:N.909, H:K.926 Salt bridges: H:K.362, H:H.587, H:H.587, H:D.729, H:H.834, H:H.834 pi-Stacking: H:Y.925 MGD.89: 39 residues within 4Å: Chain H: C.268, K.302, C.391, Q.392, I.424, G.425, N.427, E.430, S.431, H.432, A.453, D.454, I.455, R.456, H.458, R.471, A.472, G.473, D.475, A.548, M.549, G.550, H.554, G.586, H.587, N.825, N.826, G.827, R.828, L.829, L.830, H.832, F.833, H.834, Y.897, K.926 Ligands: MGD.88, 4MO.90, H2S.91 26 PLIP interactions: 26 interactions with chain H Hydrogen bonds: H:K.302, H:G.425, H:N.427, H:N.427, H:S.431, H:S.431, H:A.453, H:I.455, H:R.456, H:G.473, H:M.549, H:G.550, H:N.825, H:R.828, H:R.828, H:H.832, H:H.832, H:H.834, H:H.834, H:Y.897 Salt bridges: H:H.432, H:D.475, H:R.828, H:R.828, H:K.926 pi-Stacking: H:H.834

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

4MO.21: 4 residues within 4Å: Chain B: C.391 Ligands: MGD.19, MGD.20, H2S.22 No protein-ligand interaction detected (PLIP) 4MO.44: 4 residues within 4Å: Chain D: C.391 Ligands: MGD.42, MGD.43, H2S.45 No protein-ligand interaction detected (PLIP) 4MO.67: 4 residues within 4Å: Chain F: C.391 Ligands: MGD.65, MGD.66, H2S.68 No protein-ligand interaction detected (PLIP) 4MO.90: 4 residues within 4Å: Chain H: C.391 Ligands: MGD.88, MGD.89, H2S.91 No protein-ligand interaction detected (PLIP)

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.22: 7 residues within 4Å: Chain B: C.387, C.391, H.587, V.590 Ligands: MGD.19, MGD.20, 4MO.21 No protein-ligand interaction detected (PLIP) H2S.45: 7 residues within 4Å: Chain D: C.387, C.391, H.587, V.590 Ligands: MGD.42, MGD.43, 4MO.44 No protein-ligand interaction detected (PLIP) H2S.68: 7 residues within 4Å: Chain F: C.387, C.391, H.587, V.590 Ligands: MGD.65, MGD.66, 4MO.67 No protein-ligand interaction detected (PLIP) H2S.91: 7 residues within 4Å: Chain H: C.387, C.391, H.587, V.590 Ligands: MGD.88, MGD.89, 4MO.90 No protein-ligand interaction detected (PLIP)

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

MQ7.23: 22 residues within 4Å: Chain B: 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, S.247 Chain D: I.246 Chain E: L.67 Ligands: 01.25, 01.27, MQ7.46, 01.50, MQ7.92 16 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: B:L.97, B:Y.98, B:T.100, B:V.101, B:L.218, B:T.233, B:K.234, B:Y.240, B:I.243, B:I.243, B:L.244, D:I.246, E:L.67, E:L.67 Hydrogen bonds: B:T.100, B:K.234 MQ7.46: 22 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, S.247 Chain F: I.246 Chain G: L.67 Ligands: MQ7.23, 01.48, 01.50, MQ7.69, 01.73 16 PLIP interactions: 13 interactions with chain D, 2 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: D:L.97, D:Y.98, D:T.100, D:V.101, D:L.218, D:T.233, D:K.234, D:Y.240, D:I.243, D:I.243, D:L.244, G:L.67, G:L.67, F:I.246 Hydrogen bonds: D:T.100, D:K.234 MQ7.69: 22 residues within 4Å: Chain A: L.67 Chain F: 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, S.247 Chain H: I.246 Ligands: 01.2, MQ7.46, 01.71, 01.73, MQ7.92 16 PLIP interactions: 13 interactions with chain F, 1 interactions with chain H, 2 interactions with chain A Hydrophobic interactions: F:L.97, F:Y.98, F:T.100, F:V.101, F:L.218, F:T.233, F:K.234, F:Y.240, F:I.243, F:I.243, F:L.244, H:I.246, A:L.67, A:L.67 Hydrogen bonds: F:T.100, F:K.234 MQ7.92: 22 residues within 4Å: Chain B: I.246 Chain C: L.67 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, S.247 Ligands: 01.2, 01.13, MQ7.23, 01.27, MQ7.69 16 PLIP interactions: 13 interactions with chain H, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: H:L.97, H:Y.98, H:T.100, H:V.101, H:L.218, H:T.233, H:K.234, H:Y.240, H:I.243, H:I.243, H:L.244, C:L.67, C:L.67, B:I.246 Hydrogen bonds: H:T.100, H:K.234

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: ACEG
Probable oxidoreductase YjgC: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Uncharacterized protein YjgD

Probable oxidoreductase YjgC

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