SMTL ID : 7npa.1 (3 other biounits)

Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: A.16, R.56, L.158, P.159, C.160, C.201, T.202, E.203, K.204, C.256, C.259, K.315, R.318 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.160, A:C.201, A:C.256, A:C.259 SF4.2: 13 residues within 4Å: Chain A: W.4, C.25, P.26, N.27, L.30, L.38, C.42, R.44, G.46, N.47, G.48, C.50, E.180 8 PLIP interactions: 8 interactions with chain A, Salt bridges: A:E.180, A:E.180, A:E.180 Metal complexes: A:C.25, A:C.42, A:C.50, A:E.180, A:E.180 SF4.3: 13 residues within 4Å: Chain A: P.488, C.505, I.507, A.509, I.510, T.519, C.524, I.525, G.526, C.527, G.528, C.530 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.505, A:C.524, A:C.527, A:C.530 SF4.4: 12 residues within 4Å: Chain A: C.428, P.429, C.434, S.436, G.437, S.466, G.467, C.468, N.470, K.471, C.472 Ligands: SRM.32 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.428, A:C.434, A:C.468, A:C.472 SF4.5: 14 residues within 4Å: Chain A: C.495, N.496, G.497, C.498, G.499, R.500, C.501, I.512, S.517, C.534, P.535, N.536, G.538, R.539 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.495, A:C.498, A:C.501, A:C.534 SF4.7: 14 residues within 4Å: Chain A: L.6, V.10, C.15, A.16, K.17, C.18, G.19, T.20, C.21, F.32, P.36, C.54, P.55, R.56 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.15, A:C.18, A:C.21, A:C.54 SF4.24: 13 residues within 4Å: Chain B: A.16, R.56, L.158, P.159, C.160, C.201, T.202, E.203, K.204, C.256, C.259, K.315, R.318 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.160, B:C.201, B:C.256, B:C.259 SF4.25: 14 residues within 4Å: Chain B: W.4, C.25, P.26, N.27, L.30, L.38, C.42, R.44, G.46, N.47, G.48, C.50, E.180 Ligands: EDO.33 8 PLIP interactions: 8 interactions with chain B, Salt bridges: B:E.180, B:E.180, B:E.180 Metal complexes: B:C.25, B:C.42, B:C.50, B:E.180, B:E.180 SF4.26: 14 residues within 4Å: Chain B: P.488, C.505, I.507, A.509, I.510, T.519, C.524, I.525, G.526, C.527, G.528, K.529, C.530 Ligands: EDO.36 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.505, B:C.524, B:C.527, B:C.530 SF4.27: 12 residues within 4Å: Chain B: C.428, P.429, C.434, S.436, G.437, S.466, G.467, C.468, N.470, K.471, C.472 Ligands: SRM.9 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.428, B:C.434, B:C.468, B:C.472 SF4.28: 14 residues within 4Å: Chain B: C.495, N.496, G.497, C.498, G.499, R.500, C.501, I.512, S.517, C.534, P.535, N.536, G.538, R.539 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.495, B:C.498, B:C.501, B:C.534 SF4.30: 13 residues within 4Å: Chain B: L.6, V.10, C.15, A.16, K.17, C.18, G.19, C.21, F.32, P.36, C.54, P.55, R.56 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.15, B:C.18, B:C.21, B:C.54 SF4.53: 13 residues within 4Å: Chain C: A.16, R.56, L.158, P.159, C.160, C.201, T.202, E.203, K.204, C.256, C.259, K.315, R.318 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.160, C:C.201, C:C.256, C:C.259 SF4.54: 12 residues within 4Å: Chain C: W.4, C.25, P.26, N.27, L.30, C.42, R.44, G.46, N.47, G.48, C.50, E.180 8 PLIP interactions: 8 interactions with chain C, Salt bridges: C:E.180, C:E.180, C:E.180 Metal complexes: C:C.25, C:C.42, C:C.50, C:E.180, C:E.180 SF4.55: 13 residues within 4Å: Chain C: P.488, C.505, I.507, A.509, I.510, T.519, C.524, I.525, G.526, C.527, G.528, C.530 Ligands: EDO.62 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.505, C:C.524, C:C.527, C:C.530 SF4.56: 12 residues within 4Å: Chain C: C.428, P.429, C.434, S.436, G.437, S.466, G.467, C.468, N.470, K.471, C.472 Ligands: SRM.84 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.428, C:C.434, C:C.468, C:C.472 SF4.57: 14 residues within 4Å: Chain C: C.495, N.496, G.497, C.498, G.499, R.500, C.501, I.512, S.517, C.534, P.535, N.536, G.538, R.539 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.495, C:C.498, C:C.501, C:C.534 SF4.59: 13 residues within 4Å: Chain C: L.6, V.10, C.15, A.16, K.17, C.18, G.19, C.21, F.32, P.36, C.54, P.55, R.56 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.15, C:C.18, C:C.21, C:C.54 SF4.76: 13 residues within 4Å: Chain D: A.16, R.56, L.158, P.159, C.160, C.201, T.202, E.203, K.204, C.256, C.259, K.315, R.318 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.160, D:C.201, D:C.256, D:C.259 SF4.77: 13 residues within 4Å: Chain D: W.4, C.25, P.26, N.27, L.30, L.38, C.42, R.44, G.46, N.47, G.48, C.50, E.180 8 PLIP interactions: 8 interactions with chain D, Salt bridges: D:E.180, D:E.180, D:E.180 Metal complexes: D:C.25, D:C.42, D:C.50, D:E.180, D:E.180 SF4.78: 11 residues within 4Å: Chain D: P.488, C.505, I.507, I.510, T.519, C.524, I.525, G.526, C.527, G.528, C.530 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.505, D:C.524, D:C.527, D:C.530 SF4.79: 12 residues within 4Å: Chain D: C.428, P.429, C.434, S.436, G.437, S.466, G.467, C.468, N.470, K.471, C.472 Ligands: SRM.61 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.428, D:C.434, D:C.468, D:C.472 SF4.80: 14 residues within 4Å: Chain D: C.495, N.496, G.497, C.498, G.499, R.500, C.501, I.512, S.517, C.534, P.535, N.536, G.538, R.539 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.495, D:C.498, D:C.501, D:C.534 SF4.82: 13 residues within 4Å: Chain D: L.6, V.10, C.15, A.16, K.17, C.18, G.19, C.21, F.32, P.36, C.54, P.55, R.56 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.15, D:C.18, D:C.21, D:C.54

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

FAD.6: 32 residues within 4Å: Chain A: G.83, Q.84, D.85, G.86, G.87, V.88, V.89, T.90, V.107, V.108, T.129, T.130, K.131, S.132, K.133, Y.134, T.135, S.137, V.156, L.158, Q.161, L.199, L.200, C.201, T.202, E.203, F.262, V.271, G.272, C.273, V.274, S.281 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:Y.134, A:L.158, A:L.199 Hydrogen bonds: A:Q.84, A:D.85, A:G.87, A:V.88, A:V.89, A:T.90, A:T.90, A:V.108, A:T.129, A:K.131, A:S.132, A:S.132, A:K.133, A:K.133, A:Y.134, A:Y.134, A:S.137, A:T.202, A:C.273, A:V.274, A:S.281, A:S.281 Water bridges: A:Q.84, A:T.90, A:T.129, A:T.202, A:T.202, A:E.203 FAD.29: 33 residues within 4Å: Chain B: G.83, Q.84, D.85, G.86, G.87, V.88, V.89, T.90, V.107, V.108, T.129, T.130, K.131, S.132, K.133, Y.134, T.135, S.137, V.156, L.158, Q.161, L.199, L.200, C.201, T.202, E.203, K.204, F.262, V.271, G.272, C.273, V.274, S.281 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.134, B:L.158, B:K.204 Hydrogen bonds: B:Q.84, B:D.85, B:D.85, B:G.87, B:V.88, B:V.89, B:T.90, B:V.108, B:T.129, B:K.131, B:S.132, B:S.132, B:K.133, B:K.133, B:Y.134, B:S.137, B:T.202, B:C.273, B:V.274, B:S.281, B:S.281 Water bridges: B:Q.84, B:D.228 pi-Stacking: B:Y.134 FAD.58: 32 residues within 4Å: Chain C: G.83, Q.84, D.85, G.86, G.87, V.88, V.89, T.90, V.107, V.108, T.129, T.130, K.131, S.132, K.133, Y.134, T.135, S.137, V.156, L.158, Q.161, L.199, L.200, C.201, T.202, E.203, F.262, V.271, G.272, C.273, V.274, S.281 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:Y.134, C:L.158, C:L.199 Hydrogen bonds: C:Q.84, C:D.85, C:G.87, C:V.88, C:V.89, C:T.90, C:T.90, C:V.108, C:T.129, C:K.131, C:S.132, C:S.132, C:K.133, C:K.133, C:Y.134, C:Y.134, C:S.137, C:T.202, C:C.273, C:V.274, C:S.281, C:S.281 Water bridges: C:Q.84, C:T.90, C:T.129, C:T.202, C:T.202, C:E.203 FAD.81: 32 residues within 4Å: Chain D: G.83, Q.84, D.85, G.86, G.87, V.88, V.89, T.90, V.107, V.108, T.129, T.130, K.131, S.132, K.133, Y.134, T.135, S.137, V.156, L.158, Q.161, L.199, L.200, C.201, T.202, E.203, F.262, V.271, G.272, C.273, V.274, S.281 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:Y.134, D:L.158, D:L.199 Hydrogen bonds: D:Q.84, D:D.85, D:D.85, D:G.87, D:V.88, D:V.89, D:T.90, D:V.108, D:T.129, D:K.131, D:S.132, D:S.132, D:K.133, D:K.133, D:Y.134, D:S.137, D:T.202, D:C.273, D:V.274, D:S.281, D:S.281 Water bridges: D:Q.84, D:D.228 pi-Stacking: D:Y.134

40 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 7 residues within 4Å: Chain A: A.145, G.146, G.149, L.150, K.189, L.190, P.191 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: V.558, E.560 Chain B: V.558, E.560 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.556, E.557, R.592 Chain B: K.506, I.507 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: F.319, V.323, W.337, E.402 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: V.504, C.505, K.506, I.507, C.527, K.529 Ligands: SF4.3 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Y.586, R.601, I.602 Chain D: K.542 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.169, Y.170, Y.173 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: N.440, I.447, F.546 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: K.176 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: K.294, N.295, I.297, E.298 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: K.532, A.533, C.534, P.535 Chain B: N.47 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain B: A.145, G.146, G.149, L.150, K.189, L.190, P.191 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain B: N.27, I.29, E.41, C.42, L.43, R.44 Ligands: SF4.25 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain A: K.506, I.507 Chain B: R.556, E.557, R.592 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: G.435, S.436, G.437, L.438, C.527, G.528, K.529 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: V.504, C.505, K.506, I.507, K.529 Ligands: SF4.26 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: E.331, K.332, V.333, F.335, F.399 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: Y.2, W.4, N.7, P.36, K.37, L.38 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: E.68, R.166, Q.169, Y.170 Ligands: EDO.42 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain B: Q.169, Y.170, Y.173 Ligands: EDO.41 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: Y.237, G.240, E.242 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: L.190, P.191, K.192, I.193 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: K.294, N.295, A.296, I.297, E.298 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain C: A.145, G.146, G.149, L.150, K.189, L.190, P.191 Ligand excluded by PLIP EDO.62: 8 residues within 4Å: Chain C: V.504, C.505, K.506, I.507, C.527, K.529 Chain D: R.556 Ligands: SF4.55 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain C: R.556, E.557, R.592 Chain D: K.506, I.507 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain C: F.319, K.320, W.337, E.402 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain C: N.440, E.443, L.444, I.447, F.546, V.569 Ligand excluded by PLIP EDO.67: 4 residues within 4Å: Chain C: N.295, A.296, I.297, E.298 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain C: L.252, K.257, R.318 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain C: K.5, N.47 Chain D: K.532, A.533, C.534, P.535 Ligand excluded by PLIP EDO.83: 7 residues within 4Å: Chain D: A.145, G.146, G.149, L.150, K.189, L.190, P.191 Ligand excluded by PLIP EDO.85: 5 residues within 4Å: Chain C: K.506, I.507 Chain D: R.556, E.557, R.592 Ligand excluded by PLIP EDO.86: 5 residues within 4Å: Chain D: P.360, K.446, E.449, D.450, K.453 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain D: E.68, Q.169, Y.170 Ligands: EDO.88 Ligand excluded by PLIP EDO.88: 4 residues within 4Å: Chain D: Q.169, Y.170, Y.173 Ligands: EDO.87 Ligand excluded by PLIP EDO.89: 5 residues within 4Å: Chain D: N.440, E.443, L.444, I.447, F.546 Ligand excluded by PLIP EDO.90: 4 residues within 4Å: Chain D: K.294, N.295, A.296, I.297 Ligand excluded by PLIP EDO.91: 6 residues within 4Å: Chain C: K.532, A.533, C.534, P.535 Chain D: K.5, N.47 Ligand excluded by PLIP EDO.92: 3 residues within 4Å: Chain D: K.585, Y.586, K.588 Ligand excluded by PLIP

4 x SRM: SIROHEME(Non-covalent)

SRM.9: 29 residues within 4Å: Chain A: F.353, R.355, K.384, T.386, N.387, R.388, A.390, E.392, H.394, S.417, Y.459, K.460, K.462, K.553, T.554, G.555, R.556, R.594 Chain B: C.428, P.429, C.434, S.436, N.470, C.472, R.474, K.506 Ligands: SO4.19, H2S.20, SF4.27 45 PLIP interactions: 35 interactions with chain A, 10 interactions with chain B, Hydrophobic interactions: A:F.353, A:F.353, A:T.386, A:R.388, B:N.470 Hydrogen bonds: A:R.355, A:T.386, A:N.387, A:N.387, A:S.417, A:Y.459, A:Y.459, A:T.554, A:R.556, B:G.435, B:S.436, B:S.436 Water bridges: A:K.176, A:K.176, A:K.384, A:K.384, A:N.387, A:R.556, A:R.556, B:R.474, B:K.506, B:K.506 Salt bridges: A:R.355, A:K.384, A:R.388, A:H.394, A:K.460, A:K.462, A:K.462, A:H.478, A:K.553, A:R.556, A:R.556, A:R.594, A:R.594, B:R.474, B:K.506 pi-Cation interactions: A:K.460, A:K.462 Metal complexes: B:C.472 SRM.32: 29 residues within 4Å: Chain A: C.428, P.429, C.434, S.436, N.470, C.472, R.474, K.506 Chain B: F.353, R.355, K.384, T.386, N.387, R.388, A.390, E.392, H.394, S.417, Y.459, K.460, K.462, K.553, T.554, G.555, R.556, R.594 Ligands: SF4.4, SO4.47, H2S.49 51 PLIP interactions: 13 interactions with chain A, 38 interactions with chain B, Hydrophobic interactions: A:N.470, B:F.353, B:F.353, B:T.386, B:R.388 Hydrogen bonds: A:S.436, A:S.436, B:R.355, B:T.386, B:T.386, B:N.387, B:N.387, B:S.417, B:Y.459, B:Y.459, B:T.554, B:R.556 Water bridges: A:G.435, A:G.435, A:G.435, A:S.436, A:R.474, A:K.506, A:K.506, B:K.176, B:K.176, B:R.355, B:K.384, B:K.384, B:N.387, B:T.554, B:R.556, B:R.556 Salt bridges: A:R.474, A:K.506, B:R.355, B:K.384, B:R.388, B:H.394, B:K.460, B:K.462, B:K.462, B:H.478, B:K.553, B:R.556, B:R.556, B:R.594, B:R.594 Metal complexes: A:C.472 pi-Cation interactions: B:K.460, B:K.462 SRM.61: 30 residues within 4Å: Chain C: F.353, R.355, K.384, T.386, N.387, R.388, A.390, E.392, H.394, S.417, Y.459, K.460, K.462, K.553, T.554, G.555, R.556, R.594 Chain D: A.427, C.428, P.429, C.434, S.436, N.470, C.472, R.474, K.506 Ligands: SO4.70, H2S.71, SF4.79 48 PLIP interactions: 35 interactions with chain C, 13 interactions with chain D, Hydrophobic interactions: C:F.353, C:F.353, C:T.386, C:R.388, D:N.470 Hydrogen bonds: C:R.355, C:T.386, C:N.387, C:N.387, C:S.417, C:Y.459, C:Y.459, C:T.554, C:R.556, D:S.436, D:S.436 Water bridges: C:K.176, C:K.176, C:K.384, C:K.384, C:N.387, C:R.556, C:R.556, D:G.435, D:G.435, D:G.435, D:S.436, D:R.474, D:K.506, D:K.506 Salt bridges: C:R.355, C:K.384, C:R.388, C:H.394, C:K.460, C:K.462, C:K.462, C:H.478, C:K.553, C:R.556, C:R.556, C:R.594, C:R.594, D:R.474, D:K.506 pi-Cation interactions: C:K.460, C:K.462 Metal complexes: D:C.472 SRM.84: 29 residues within 4Å: Chain C: C.428, P.429, C.434, S.436, N.470, C.472, R.474, K.506 Chain D: F.353, R.355, K.384, T.386, N.387, R.388, A.390, E.392, H.394, S.417, Y.459, K.460, K.462, K.553, T.554, G.555, R.556, R.594 Ligands: SF4.56, SO4.93, H2S.96 51 PLIP interactions: 37 interactions with chain D, 14 interactions with chain C, Hydrophobic interactions: D:F.353, D:F.353, D:T.386, D:R.388, C:N.470 Hydrogen bonds: D:R.355, D:T.386, D:T.386, D:N.387, D:N.387, D:S.417, D:Y.459, D:Y.459, D:T.554, D:R.556, C:S.436, C:S.436 Water bridges: D:K.176, D:K.176, D:R.355, D:K.384, D:K.384, D:N.387, D:K.553, D:T.554, D:R.556, C:G.435, C:G.435, C:G.435, C:G.435, C:S.436, C:R.474, C:K.506, C:K.506 Salt bridges: D:R.355, D:K.384, D:R.388, D:H.394, D:K.460, D:K.462, D:K.462, D:K.553, D:R.556, D:R.556, D:R.594, D:R.594, C:R.474, C:K.506 pi-Cation interactions: D:K.460, D:K.462 Metal complexes: C:C.472

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

SO4.19: 7 residues within 4Å: Chain A: K.176, E.418, G.419, R.423, K.460, Q.591 Ligands: SRM.9 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.419, A:G.419 Water bridges: A:K.176, A:K.176, A:K.176, A:K.176, A:K.176, A:K.176, A:K.176, A:K.176, A:K.176, A:R.423, A:R.423 Salt bridges: A:K.176, A:R.423, A:K.460 SO4.47: 5 residues within 4Å: Chain B: G.419, R.423, K.460 Ligands: SRM.32, H2S.49 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.419 Water bridges: B:K.176, B:K.176, B:K.176, B:K.176, B:K.176, B:K.176, B:K.176, B:R.423, B:R.423, B:R.423, B:R.423, B:R.423, B:Q.591 Salt bridges: B:K.176, B:R.423, B:K.460 SO4.48: 4 residues within 4Å: Chain B: K.230, K.231, C.273, V.274 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.231 Water bridges: B:K.231, B:K.231, B:G.232, B:G.275 Salt bridges: B:K.231 SO4.70: 5 residues within 4Å: Chain C: G.419, R.423, K.460 Ligands: SRM.61, H2S.71 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:G.419 Water bridges: C:K.176, C:K.176, C:K.176, C:K.176, C:K.176, C:K.176, C:K.176, C:E.418, C:E.418, C:R.423, C:R.423, C:R.423, C:R.423, C:Q.591 Salt bridges: C:K.176, C:R.423, C:K.460 SO4.93: 6 residues within 4Å: Chain D: K.176, G.419, R.423, K.460 Ligands: SRM.84, H2S.96 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.419 Water bridges: D:K.176, D:K.176, D:K.176, D:K.176, D:K.176, D:K.176, D:K.176, D:K.176, D:R.423, D:R.423, D:R.423 Salt bridges: D:K.176, D:R.423, D:K.460 SO4.94: 4 residues within 4Å: Chain D: K.230, K.231, C.273, V.274 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.231 Water bridges: D:G.275, D:D.278 SO4.95: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.20: 4 residues within 4Å: Chain A: R.423, K.460, K.462 Ligands: SRM.9 No protein-ligand interaction detected (PLIP) H2S.49: 5 residues within 4Å: Chain B: R.423, K.460, K.462 Ligands: SRM.32, SO4.47 No protein-ligand interaction detected (PLIP) H2S.71: 5 residues within 4Å: Chain C: R.423, K.460, K.462 Ligands: SRM.61, SO4.70 No protein-ligand interaction detected (PLIP) H2S.96: 5 residues within 4Å: Chain D: R.423, K.460, K.462 Ligands: SRM.84, SO4.93 No protein-ligand interaction detected (PLIP)

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

CL.21: 3 residues within 4Å: Chain A: R.56, C.160, N.163 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain A: R.67, Y.173, A.457, P.458, H.584 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain B: R.56, C.160, N.163 Ligand excluded by PLIP CL.51: 5 residues within 4Å: Chain B: R.67, Y.173, A.457, P.458, H.584 Ligand excluded by PLIP CL.72: 3 residues within 4Å: Chain C: R.56, C.160, N.163 Ligand excluded by PLIP CL.73: 5 residues within 4Å: Chain C: R.67, Y.173, A.457, P.458, H.584 Ligand excluded by PLIP CL.97: 3 residues within 4Å: Chain D: R.56, C.160, N.163 Ligand excluded by PLIP CL.98: 5 residues within 4Å: Chain D: R.67, Y.173, A.457, P.458, H.584 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.39: 3 residues within 4Å: Chain B: W.363, N.433 Ligands: GOL.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.347 Water bridges: A:R.347 GOL.40: 3 residues within 4Å: Chain B: W.363, N.433 Ligands: GOL.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.433, B:N.433 Water bridges: B:T.442 GOL.46: 4 residues within 4Å: Chain B: K.542 Chain C: K.588, R.601, I.602 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.588, C:R.601 Water bridges: C:R.601, B:K.542 GOL.52: 4 residues within 4Å: Chain B: Y.586, K.588, R.601 Chain C: K.542 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.542, B:K.588 Water bridges: B:K.606, B:K.606 GOL.64: 4 residues within 4Å: Chain C: D.110, C.112, W.113, E.225 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:C.112, C:W.113 Water bridges: C:T.130, C:K.133

1 x LI: LITHIUM ION(Non-covalent)

LI.74: 6 residues within 4Å: Chain A: D.511, I.512, R.513 Chain C: D.511, I.512, R.513 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.511, C:I.512, A:D.511, A:I.512

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.75: 4 residues within 4Å: Chain C: R.347 Chain D: W.363, N.433, T.442 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.433, C:R.347 Water bridges: D:E.431, D:N.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jespersen, M. et al., Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales. Nat.Chem.Biol. (2023)

Release Date

2022-03-23

Peptides

Coenzyme F420-dependent sulfite reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Coenzyme F420-dependent sulfite reductase

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