- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 24 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 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
32 PLIP interactions:32 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, A:E.203, A:E.203
- pi-Stacking: A:Y.134
FAD.27: 31 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, F.262, V.271, G.272, C.273, V.274, S.281
28 PLIP interactions:28 interactions with chain B- Hydrophobic interactions: B:Y.134, B:L.158, B:L.199
- 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:T.90, B:T.129, B:D.228
FAD.48: 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
32 PLIP interactions:32 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: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:E.203, C:E.203
- pi-Stacking: C:Y.134
FAD.74: 33 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, K.204, F.262, V.271, G.272, C.273, V.274, S.281
31 PLIP interactions:31 interactions with chain D- Hydrophobic interactions: D:Y.134, 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:Q.84, D:T.90, D:T.129, D:E.203, D:E.203
- 29 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: 5 residues within 4Å:- Chain A: R.556, E.557, R.592
- Chain B: K.506, I.507
Ligand excluded by PLIPEDO.11: 6 residues within 4Å:- Chain A: K.5, N.47
- Chain B: K.532, A.533, C.534, P.535
Ligand excluded by PLIPEDO.12: 6 residues within 4Å:- Chain A: N.440, E.443, L.444, I.447, F.546, V.569
Ligand excluded by PLIPEDO.13: 4 residues within 4Å:- Chain A: K.585, Y.586, K.588
- Ligands: EDO.16
Ligand excluded by PLIPEDO.15: 5 residues within 4Å:- Chain A: L.168, Q.169, P.191, K.192, I.193
Ligand excluded by PLIPEDO.16: 4 residues within 4Å:- Chain A: K.588, R.601
- Chain D: K.542
- Ligands: EDO.13
Ligand excluded by PLIPEDO.17: 7 residues within 4Å:- Chain A: V.504, C.505, K.506, I.507, C.527, K.529
- Ligands: SF4.3
Ligand excluded by PLIPEDO.29: 7 residues within 4Å:- Chain B: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.31: 6 residues within 4Å:- Chain A: K.506, I.507
- Chain B: R.556, E.557, R.592
- Ligands: EDO.33
Ligand excluded by PLIPEDO.32: 7 residues within 4Å:- Chain B: V.504, C.505, K.506, I.507, C.527, K.529
- Ligands: SF4.24
Ligand excluded by PLIPEDO.33: 6 residues within 4Å:- Chain A: K.506, I.507
- Chain B: R.556, E.557, R.592
- Ligands: EDO.31
Ligand excluded by PLIPEDO.34: 5 residues within 4Å:- Chain B: N.440, E.443, L.444, I.447, F.546
Ligand excluded by PLIPEDO.50: 7 residues within 4Å:- Chain C: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.52: 5 residues within 4Å:- Chain C: R.556, E.557, R.592
- Chain D: K.506, I.507
Ligand excluded by PLIPEDO.53: 5 residues within 4Å:- Chain C: E.68, R.166, Q.169, Y.170
- Ligands: EDO.56
Ligand excluded by PLIPEDO.54: 5 residues within 4Å:- Chain C: K.294, N.295, A.296, I.297, E.298
Ligand excluded by PLIPEDO.55: 6 residues within 4Å:- Chain C: V.504, C.505, K.506, I.507, C.527
- Ligands: SF4.45
Ligand excluded by PLIPEDO.56: 4 residues within 4Å:- Chain C: Q.169, Y.170, Y.173
- Ligands: EDO.53
Ligand excluded by PLIPEDO.57: 5 residues within 4Å:- Chain C: N.440, E.443, I.447, F.546, V.569
Ligand excluded by PLIPEDO.58: 4 residues within 4Å:- Chain C: K.585, Y.586, K.588
- Ligands: GOL.35
Ligand excluded by PLIPEDO.59: 3 residues within 4Å:- Chain C: L.566, S.568, E.571
Ligand excluded by PLIPEDO.60: 4 residues within 4Å:- Chain C: M.49, L.168, F.171, Q.172
Ligand excluded by PLIPEDO.62: 5 residues within 4Å:- Chain C: F.319, K.320, V.323, W.337, E.402
Ligand excluded by PLIPEDO.63: 6 residues within 4Å:- Chain C: K.5, N.47
- Chain D: K.532, A.533, C.534, P.535
Ligand excluded by PLIPEDO.76: 7 residues within 4Å:- Chain D: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.78: 5 residues within 4Å:- Chain C: K.506, I.507
- Chain D: R.556, E.557, R.592
Ligand excluded by PLIPEDO.79: 3 residues within 4Å:- Chain D: I.559, A.597, A.600
Ligand excluded by PLIPEDO.80: 6 residues within 4Å:- Chain D: N.440, E.443, L.444, I.447, F.546, V.569
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: A.427, C.428, P.429, C.434, S.436, N.470, C.472, R.474, K.506
- Ligands: SO4.18, H2S.19, SF4.25
45 PLIP interactions:13 interactions with chain B, 32 interactions with chain A,- Hydrophobic interactions: B:N.470, A:F.353, A:T.386, A:R.388
- Hydrogen bonds: B:S.436, B:S.436, A:R.355, A:T.386, A:N.387, A:N.387, A:S.417, A:T.554, A:R.556
- Water bridges: B:G.435, B:G.435, B:G.435, B:N.470, B:R.474, B:K.506, B:K.506, A:K.176, A:K.176, A:K.384, A:K.384, A:N.387, A:R.556, A:R.556
- Salt bridges: B:R.474, B:K.506, 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
- Metal complexes: B:C.472
- pi-Cation interactions: A:K.460, A:K.462
SRM.30: 30 residues within 4Å:- Chain A: A.427, 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, SO4.36, H2S.40
50 PLIP interactions:13 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: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:N.470, 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: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.51: 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: SO4.64, H2S.65, SF4.72
47 PLIP interactions:14 interactions with chain D, 33 interactions with chain C,- Hydrophobic interactions: D:N.470, C:F.353, C:T.386, C:R.388
- Hydrogen bonds: D:S.436, D:S.436, C:R.355, C:T.386, C:N.387, C:N.387, C:S.417, C:T.554, C:R.556
- Water bridges: D:G.435, D:G.435, D:G.435, D:S.436, D:N.470, D:R.474, D:K.506, D:K.506, C:K.176, C:K.176, C:K.384, C:K.384, C:N.387, C:R.556, C:R.556, C:R.556
- Salt bridges: D:R.474, D:K.506, 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
- Metal complexes: D:C.472
- pi-Cation interactions: C:K.460, C:K.462
SRM.77: 30 residues within 4Å:- Chain C: 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: SF4.46, SO4.82, H2S.83
48 PLIP interactions:11 interactions with chain C, 37 interactions with chain D,- Hydrophobic interactions: C:N.470, D:F.353, D:F.353, D:T.386, D:R.388
- Hydrogen bonds: C:S.436, C:S.436, 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
- Water bridges: C:G.435, C:G.435, C:G.435, C:R.474, C:K.506, D:K.176, D:K.176, D:K.384, D:K.384, D:N.387, D:T.554, D:R.556, D:R.556
- Salt bridges: C:R.474, C:K.506, 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
- Metal complexes: C:C.472
- pi-Cation interactions: D:K.460, D:K.462
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.14: 2 residues within 4Å:- Chain A: W.363, N.433
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.433
GOL.35: 5 residues within 4Å:- Chain B: K.542
- Chain C: K.588, R.601, I.602
- Ligands: EDO.58
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain C- Hydrogen bonds: B:K.542, B:K.542, C:K.588, C:K.588, C:R.601
GOL.61: 3 residues within 4Å:- Chain C: W.363, N.433, T.442
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.433
- Water bridges: C:N.440
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.18: 5 residues within 4Å:- Chain A: G.419, R.423, K.460
- Ligands: SRM.9, H2S.19
19 PLIP interactions:19 interactions with chain A- Hydrogen bonds: 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:E.418, A:E.418, 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
SO4.36: 7 residues within 4Å:- Chain B: K.176, E.418, G.419, R.423, K.460, Q.591
- Ligands: SRM.30
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:E.418, B:R.423, B:R.423, B:R.423
- Salt bridges: B:K.176, B:R.423, B:K.460
SO4.37: 4 residues within 4Å:- Chain B: K.230, K.231, C.273, V.274
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.231
- Water bridges: B:G.275
SO4.38: 5 residues within 4Å:- Chain B: Y.586, K.588, R.601
- Chain C: K.542
- Ligands: SO4.39
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain C- Water bridges: B:R.601, C:K.542
- Salt bridges: B:K.588, B:R.601, C:K.542
SO4.39: 4 residues within 4Å:- Chain B: K.585, Y.586, K.588
- Ligands: SO4.38
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:K.588
SO4.64: 5 residues within 4Å:- Chain C: G.419, R.423, K.460
- Ligands: SRM.51, H2S.65
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:E.418, C:E.418, C:R.423, C:R.423, C:Q.591
- Salt bridges: C:K.176, C:R.423, C:K.460
SO4.81: 4 residues within 4Å:- Chain A: K.542
- Chain D: Y.586, K.588, R.601
8 PLIP interactions:5 interactions with chain D, 3 interactions with chain A- Water bridges: D:K.588, D:K.588, D:R.601, A:K.542, A:K.542
- Salt bridges: D:K.588, D:R.601, A:K.542
SO4.82: 7 residues within 4Å:- Chain D: K.176, E.418, G.419, R.423, K.460, Q.591
- Ligands: SRM.77
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:E.418, D:R.423, D:R.423, D:R.423, D:Q.591
- Salt bridges: D:K.176, D:R.423, D:K.460
- 4 x H2S: HYDROSULFURIC ACID(Non-covalent)
H2S.19: 5 residues within 4Å:- Chain A: R.423, K.460, K.462
- Ligands: SRM.9, SO4.18
No protein-ligand interaction detected (PLIP)H2S.40: 4 residues within 4Å:- Chain B: R.423, K.460, K.462
- Ligands: SRM.30
No protein-ligand interaction detected (PLIP)H2S.65: 5 residues within 4Å:- Chain C: R.423, K.460, K.462
- Ligands: SRM.51, SO4.64
No protein-ligand interaction detected (PLIP)H2S.83: 4 residues within 4Å:- Chain D: R.423, K.460, K.462
- Ligands: SRM.77
No protein-ligand interaction detected (PLIP)- 7 x CL: CHLORIDE ION(Non-functional Binders)
CL.20: 3 residues within 4Å:- Chain A: R.56, C.160, N.163
Ligand excluded by PLIPCL.21: 5 residues within 4Å:- Chain A: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.41: 5 residues within 4Å:- Chain B: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.66: 3 residues within 4Å:- Chain C: R.56, C.160, N.163
Ligand excluded by PLIPCL.67: 5 residues within 4Å:- Chain C: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.84: 3 residues within 4Å:- Chain D: R.56, C.160, N.163
Ligand excluded by PLIPCL.85: 5 residues within 4Å:- Chain D: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIP- 1 x LI: LITHIUM ION(Non-covalent)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 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
EB
FC
GD
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 24 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 29 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x SRM: SIROHEME(Non-covalent)
- 3 x GOL: GLYCEROL(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)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 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
EB
FC
GD
H