- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 25 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)
- 5 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)(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
29 PLIP interactions:29 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: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
FAD.31: 32 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, 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, V.271, G.272, C.273, V.274, S.281
- Ligands: FAD.39
24 PLIP interactions:24 interactions with chain B- Hydrophobic interactions: B:Y.134, B:Y.134, B:L.158, B:K.204
- Hydrogen bonds: B:Q.84, 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:Y.134, B:T.135, B:S.137, B:T.202, B:V.271, B:C.273, B:V.274, B:S.281
FAD.39: 29 residues within 4Å:- Chain B: G.83, Q.84, D.85, G.86, G.87, V.88, V.89, T.129, K.131, S.132, K.133, Y.134, V.156, G.157, 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, T.282
- Ligands: FAD.31
18 PLIP interactions:18 interactions with chain B- Hydrophobic interactions: B:Y.134, B:Y.134, B:L.199
- Hydrogen bonds: B:Q.84, B:D.85, B:G.86, B:G.87, B:V.88, B:V.89, B:T.129, B:K.133, B:K.133, B:S.137, B:T.202, B:C.273, B:V.274, B:S.281, B:T.282
FAD.54: 33 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, K.204, F.262, V.271, G.272, C.273, V.274, S.281
30 PLIP interactions:30 interactions with chain C- Hydrophobic interactions: C:Y.134, C:L.158, C:L.199, C:K.204
- 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: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
FAD.77: 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, 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 D- Hydrophobic interactions: D:Y.134, D:L.158, D:L.199, D:K.204
- 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:T.129, D:D.228
- 28 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 PLIPEDO.10: 8 residues within 4Å:- Chain A: V.504, C.505, K.506, I.507, C.527, K.529
- Chain B: R.556
- Ligands: SF4.3
Ligand excluded by PLIPEDO.11: 5 residues within 4Å:- Chain A: R.556, E.557, R.592
- Chain B: K.506, I.507
Ligand excluded by PLIPEDO.12: 4 residues within 4Å:- Chain A: D.450, N.451, K.453, H.455
Ligand excluded by PLIPEDO.13: 4 residues within 4Å:- Chain A: N.440, L.444, F.546, V.569
Ligand excluded by PLIPEDO.16: 6 residues within 4Å:- Chain A: K.5, N.47
- Chain B: K.532, A.533, C.534, P.535
Ligand excluded by PLIPEDO.17: 5 residues within 4Å:- Chain A: E.68, R.166, Q.169, Y.170, K.192
Ligand excluded by PLIPEDO.18: 1 residues within 4Å:- Chain A: E.225
Ligand excluded by PLIPEDO.19: 8 residues within 4Å:- Chain A: G.435, S.436, G.437, L.438, C.527, G.528, K.529, K.532
Ligand excluded by PLIPEDO.21: 3 residues within 4Å:- Chain A: P.191, K.192, I.193
Ligand excluded by PLIPEDO.22: 2 residues within 4Å:- Chain A: K.17, R.35
Ligand excluded by PLIPEDO.23: 4 residues within 4Å:- Chain A: L.566, M.567, S.568, E.571
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain A: D.511, Y.518
- Chain D: D.178, L.181
Ligand excluded by PLIPEDO.40: 5 residues within 4Å:- Chain A: K.506, I.507
- Chain B: R.556, E.557, R.592
Ligand excluded by PLIPEDO.43: 4 residues within 4Å:- Chain B: N.440, I.447, F.546, V.569
Ligand excluded by PLIPEDO.56: 7 residues within 4Å:- Chain C: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.58: 9 residues within 4Å:- Chain C: V.504, C.505, K.506, I.507, I.525, C.527, K.529
- Chain D: R.556
- Ligands: SF4.51
Ligand excluded by PLIPEDO.59: 5 residues within 4Å:- Chain C: R.556, E.557, R.592
- Chain D: K.506, I.507
Ligand excluded by PLIPEDO.60: 4 residues within 4Å:- Chain C: D.450, N.451, K.453, H.455
Ligand excluded by PLIPEDO.61: 4 residues within 4Å:- Chain C: E.68, R.166, Q.169, Y.170
Ligand excluded by PLIPEDO.62: 6 residues within 4Å:- Chain C: L.168, Q.169, L.190, P.191, K.192, I.193
Ligand excluded by PLIPEDO.63: 5 residues within 4Å:- Chain C: N.440, E.443, I.447, F.546, V.569
Ligand excluded by PLIPEDO.65: 3 residues within 4Å:- Chain C: V.10, K.17, R.35
Ligand excluded by PLIPEDO.66: 6 residues within 4Å:- Chain C: K.5, N.47
- Chain D: K.532, A.533, C.534, P.535
Ligand excluded by PLIPEDO.79: 7 residues within 4Å:- Chain D: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.81: 5 residues within 4Å:- Chain C: K.506, I.507
- Chain D: R.556, E.557, R.592
Ligand excluded by PLIPEDO.84: 5 residues within 4Å:- Chain D: F.319, V.323, W.337, F.399, E.402
Ligand excluded by PLIPEDO.85: 4 residues within 4Å:- Chain D: K.585, Y.586, K.588
- Ligands: SO4.27
Ligand excluded by PLIP- 4 x SRM: SIROHEME(Non-covalent)
SRM.9: 30 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, V.473, R.474, K.506
- Ligands: SO4.25, H2S.28, SF4.34
48 PLIP interactions:35 interactions with chain A, 13 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: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:G.435, B:G.435, B:G.435, B:S.436, 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.42: 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, SO4.46, H2S.47
49 PLIP interactions:12 interactions with chain A, 37 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:N.387, B:N.387, B:S.417, B:Y.459, B:T.554, B:R.556
- Water bridges: A:G.435, A:G.435, A:G.435, 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:S.417, B:T.554, 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: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.57: 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: C.428, P.429, C.434, S.436, N.470, C.472, V.473, R.474, K.506
- Ligands: SO4.67, H2S.69, SF4.75
46 PLIP interactions:33 interactions with chain C, 13 interactions with chain D,- Hydrophobic interactions: C:F.353, C:F.353, C:R.388, D:N.470
- Hydrogen bonds: C:R.355, C:T.386, C:N.387, C:N.387, C:S.417, 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.423, C:R.556, C:R.556, D:G.435, D:G.435, D:G.435, D:G.435, 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.80: 31 residues within 4Å:- Chain C: A.427, C.428, P.429, C.434, S.436, N.470, C.472, V.473, 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: SF4.52, SO4.86, H2S.88
48 PLIP interactions:36 interactions with chain D, 12 interactions with chain C,- Hydrophobic interactions: D:F.353, D:F.353, 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:K.384, D:K.384, D:N.387, D:T.554, D:R.556, D:R.556, C:G.435, C:N.470, C:N.470, 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:H.478, 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
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.14: 3 residues within 4Å:- Chain A: K.588, R.601
- Chain D: K.542
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain A- Hydrogen bonds: D:K.542, A:K.588, A:R.601, A:R.601
GOL.41: 10 residues within 4Å:- Chain A: R.556
- Chain B: N.470, V.504, C.505, K.506, I.507, I.525, C.527, K.529
- Ligands: SF4.33
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:N.470, B:V.504, B:K.506, B:I.507, A:R.556
GOL.45: 4 residues within 4Å:- Chain B: K.542
- Chain C: Y.586, K.588, R.601
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.588, C:R.601
GOL.64: 4 residues within 4Å:- Chain C: K.294, N.295, I.297, E.298
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:K.294
GOL.82: 6 residues within 4Å:- Chain A: I.602, K.606
- Chain D: F.487, E.543, M.547, L.566
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain D- Water bridges: A:K.606, A:K.606, D:E.543
GOL.83: 3 residues within 4Å:- Chain D: D.110, W.113, E.225
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.110, D:V.224
- Water bridges: D:D.110
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.15: 7 residues within 4Å:- Chain A: F.319, K.320, V.323, E.324, W.337, F.399, E.402
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:F.399, A:E.402, A:A.403
- Water bridges: A:E.402
PEG.20: 4 residues within 4Å:- Chain A: R.347, K.382
- Chain B: W.363, N.433
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.433
PEG.44: 5 residues within 4Å:- Chain B: K.585, Y.586, K.588, R.601
- Chain C: K.542
4 PLIP interactions:2 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:K.542, C:K.542, B:K.588, B:R.601
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.25: 5 residues within 4Å:- Chain A: K.176, G.419, R.423, K.460
- 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:E.418, A:E.418, A:R.423, A:R.423, A:Q.591
- Salt bridges: A:K.176, A:R.423, A:K.460
SO4.26: 4 residues within 4Å:- Chain A: K.230, K.231, C.273, V.274
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.231
- Water bridges: A:G.275
SO4.27: 5 residues within 4Å:- Chain A: K.542
- Chain D: Y.586, K.588, R.601
- Ligands: EDO.85
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain A- Salt bridges: D:K.588, D:R.601, A:K.542
- Water bridges: A:K.542
SO4.46: 6 residues within 4Å:- Chain B: K.176, G.419, R.423, K.460
- Ligands: SRM.42, H2S.47
16 PLIP interactions:16 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:K.176, B:R.423, B:R.423, B:R.423, B:R.423
- Salt bridges: B:K.176, B:R.423, B:K.460
SO4.67: 5 residues within 4Å:- Chain C: G.419, R.423, K.460
- Ligands: SRM.57, H2S.69
16 PLIP interactions:16 interactions with chain C- Hydrogen bonds: C:G.419, 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:K.176, C:R.423, C:R.423, C:R.423
- Salt bridges: C:K.176, C:R.423, C:K.460
SO4.68: 4 residues within 4Å:- Chain C: K.230, K.231, C.273, V.274
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:K.231
- Water bridges: C:G.232, C:G.275, C:G.275, C:D.278
SO4.86: 5 residues within 4Å:- Chain D: G.419, R.423, K.460
- Ligands: SRM.80, H2S.88
14 PLIP interactions:14 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:R.423, D:R.423, D:R.423
- Salt bridges: D:K.176, D:R.423, D:K.460
SO4.87: 5 residues within 4Å:- Chain D: K.230, K.231, C.273, V.274, G.275
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:K.231, D:G.275
- Water bridges: D:C.273, D:S.276
- 4 x H2S: HYDROSULFURIC ACID(Non-covalent)
H2S.28: 4 residues within 4Å:- Chain A: R.423, K.460, K.462
- Ligands: SRM.9
No protein-ligand interaction detected (PLIP)H2S.47: 5 residues within 4Å:- Chain B: R.423, K.460, K.462
- Ligands: SRM.42, SO4.46
No protein-ligand interaction detected (PLIP)H2S.69: 5 residues within 4Å:- Chain C: R.423, K.460, K.462
- Ligands: SRM.57, SO4.67
No protein-ligand interaction detected (PLIP)H2S.88: 5 residues within 4Å:- Chain D: R.423, K.460, K.462
- Ligands: SRM.80, SO4.86
No protein-ligand interaction detected (PLIP)- 7 x CL: CHLORIDE ION(Non-functional Binders)
CL.29: 3 residues within 4Å:- Chain A: R.56, C.160, N.163
Ligand excluded by PLIPCL.30: 5 residues within 4Å:- Chain A: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.48: 5 residues within 4Å:- Chain B: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.70: 3 residues within 4Å:- Chain C: R.56, C.160, N.163
Ligand excluded by PLIPCL.71: 5 residues within 4Å:- Chain C: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.89: 5 residues within 4Å:- Chain D: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.90: 3 residues within 4Å:- Chain D: R.56, C.160, N.163
Ligand excluded by PLIP- 1 x LI: LITHIUM ION(Non-covalent)
- 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
MB
NC
OD
P
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 25 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)
- 5 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)(Covalent)
- 28 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x SRM: SIROHEME(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 8 x SO4: SULFATE ION(Non-functional Binders)
- 4 x H2S: HYDROSULFURIC ACID(Non-covalent)
- 7 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x LI: LITHIUM ION(Non-covalent)
- 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
MB
NC
OD
P