- 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
30 PLIP interactions:30 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
- pi-Stacking: A:Y.134
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
28 PLIP interactions:28 interactions with chain B- Hydrophobic interactions: B:Y.134, B:L.158, B:L.199, 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:T.129, B:I.229
FAD.51: 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
28 PLIP interactions:28 interactions with chain C- Hydrophobic interactions: C:Y.134, C:L.158
- 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.202, C:T.202, C:E.203
FAD.73: 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
29 PLIP interactions:29 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:V.108, 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:D.228
- 26 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: 4 residues within 4Å:- Chain A: D.450, N.451, K.453, H.455
Ligand excluded by PLIPEDO.12: 2 residues within 4Å:- Chain A: W.363, N.433
Ligand excluded by PLIPEDO.13: 2 residues within 4Å:- Chain A: F.319, E.402
Ligand excluded by PLIPEDO.14: 5 residues within 4Å:- Chain A: N.440, L.444, I.447, F.546, V.569
Ligand excluded by PLIPEDO.15: 4 residues within 4Å:- Chain A: K.78, D.278, G.279, Y.280
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.18: 5 residues within 4Å:- Chain A: L.608, E.609
- Chain D: M.564, L.608, E.609
Ligand excluded by PLIPEDO.31: 7 residues within 4Å:- Chain B: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.33: 4 residues within 4Å:- Chain B: K.230, K.231, C.273, V.274
Ligand excluded by PLIPEDO.34: 4 residues within 4Å:- Chain B: E.570, E.571, N.574, N.618
Ligand excluded by PLIPEDO.35: 8 residues within 4Å:- Chain B: V.504, C.505, K.506, I.507, I.525, C.527, K.529
- Ligands: SF4.26
Ligand excluded by PLIPEDO.36: 5 residues within 4Å:- Chain B: D.450, N.451, F.452, K.453, H.455
Ligand excluded by PLIPEDO.38: 3 residues within 4Å:- Chain B: Q.169, Y.170, Y.173
Ligand excluded by PLIPEDO.39: 5 residues within 4Å:- Chain B: F.487, E.543, M.547, K.565
- Chain C: I.602
Ligand excluded by PLIPEDO.53: 7 residues within 4Å:- Chain C: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.55: 5 residues within 4Å:- Chain C: L.168, L.190, P.191, K.192, I.193
Ligand excluded by PLIPEDO.56: 5 residues within 4Å:- Chain C: R.556, E.557, R.592
- Chain D: K.506, I.507
Ligand excluded by PLIPEDO.57: 4 residues within 4Å:- Chain C: F.319, K.320, W.337, E.402
Ligand excluded by PLIPEDO.58: 7 residues within 4Å:- Chain C: V.504, C.505, K.506, I.507, C.527, K.529
- Ligands: SF4.48
Ligand excluded by PLIPEDO.59: 3 residues within 4Å:- Chain C: E.68, R.166, Q.169
Ligand excluded by PLIPEDO.61: 6 residues within 4Å:- Chain C: N.440, E.443, L.444, I.447, F.546, V.569
Ligand excluded by PLIPEDO.75: 7 residues within 4Å:- Chain D: A.145, G.146, G.149, L.150, K.189, L.190, P.191
Ligand excluded by PLIPEDO.77: 7 residues within 4Å:- Chain D: V.504, C.505, K.506, I.507, C.527, K.529
- Ligands: SF4.70
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: Y.521, N.522, C.524
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: SO4.20, H2S.21, SF4.27
47 PLIP interactions:36 interactions with chain A, 11 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, A:R.556, B:G.435, B:G.435, B:N.470, B:R.474, 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: 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, SO4.41, H2S.43
51 PLIP interactions:15 interactions with chain A, 36 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:T.554, B:R.556
- Water bridges: A:G.435, A:G.435, A:G.435, A:G.435, A:N.470, A:N.470, A:R.474, A:K.506, A:K.506, 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.54: 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: SO4.63, H2S.65, SF4.71
47 PLIP interactions:35 interactions with chain C, 12 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:R.355, 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: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: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.76: 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: SF4.49, SO4.80, H2S.83
49 PLIP interactions:12 interactions with chain C, 37 interactions with chain D,- Hydrophobic interactions: C:N.470, 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, C:K.506, D:K.176, D:K.176, D:R.355, 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
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 10 residues within 4Å:- Chain A: N.470, V.504, C.505, K.506, I.507, I.525, C.527, K.529
- Chain B: R.556
- Ligands: SF4.3
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:V.504, A:K.506, A:I.507, A:K.529, B:R.556
- Water bridges: A:N.470
GOL.17: 4 residues within 4Å:- Chain A: K.542
- Chain D: Y.586, K.588, R.601
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain A- Hydrogen bonds: D:R.601, A:K.542
- Water bridges: D:Y.586, A:E.543
GOL.37: 4 residues within 4Å:- Chain B: V.10, K.17, E.206, A.254
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:V.10, B:K.17, B:E.206
- Water bridges: B:G.255
GOL.40: 2 residues within 4Å:- Chain B: W.363, N.433
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.433, B:T.442
GOL.62: 2 residues within 4Å:- Chain C: D.110, W.113
5 PLIP interactions:5 interactions with chain C- Water bridges: C:D.110, C:C.112, C:N.128, C:N.128, C:T.130
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.20: 5 residues within 4Å:- Chain A: G.419, R.423, K.460
- Ligands: SRM.9, H2S.21
15 PLIP interactions:15 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:E.418, A:R.423, A:R.423, A:Q.591, A:Q.591
- Salt bridges: A:K.176, A:R.423, A:K.460
SO4.41: 6 residues within 4Å:- Chain B: K.176, E.418, G.419, R.423, K.460
- Ligands: SRM.32
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
SO4.42: 6 residues within 4Å:- Chain B: N.440, E.443, L.444, I.447, F.546, V.569
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.440, B:L.444
- Water bridges: B:N.440
SO4.63: 5 residues within 4Å:- Chain C: G.419, R.423, K.460
- Ligands: SRM.54, H2S.65
16 PLIP interactions:16 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:Q.591
- Salt bridges: C:K.176, C:R.423, C:K.460
SO4.64: 4 residues within 4Å:- Chain B: K.542
- Chain C: Y.586, K.588, R.601
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain B- Water bridges: C:K.588, C:R.601, C:R.601
- Salt bridges: C:K.588, C:R.601, B:K.542
SO4.80: 5 residues within 4Å:- Chain D: G.419, R.423, K.460
- Ligands: SRM.76, H2S.83
17 PLIP interactions:17 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, D:R.423, D:R.423, D:Q.591
- Salt bridges: D:K.176, D:R.423, D:K.460
SO4.81: 4 residues within 4Å:- Chain D: K.230, K.231, C.273, V.274
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:K.231
- Water bridges: D:G.275
SO4.82: 4 residues within 4Å:- Chain A: Y.586, K.588, R.601
- Chain D: K.542
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain D- Water bridges: A:K.588, A:K.588, D:K.542, D:K.542
- Salt bridges: A:K.588, A:R.601, D:K.542
- 4 x H2S: HYDROSULFURIC ACID(Non-covalent)
H2S.21: 5 residues within 4Å:- Chain A: R.423, K.460, K.462
- Ligands: SRM.9, SO4.20
No protein-ligand interaction detected (PLIP)H2S.43: 4 residues within 4Å:- Chain B: R.423, K.460, K.462
- Ligands: SRM.32
No protein-ligand interaction detected (PLIP)H2S.65: 5 residues within 4Å:- Chain C: R.423, K.460, K.462
- Ligands: SRM.54, SO4.63
No protein-ligand interaction detected (PLIP)H2S.83: 5 residues within 4Å:- Chain D: R.423, K.460, K.462
- Ligands: SRM.76, SO4.80
No protein-ligand interaction detected (PLIP)- 7 x CL: CHLORIDE ION(Non-functional Binders)
CL.22: 3 residues within 4Å:- Chain A: R.56, C.160, N.163
Ligand excluded by PLIPCL.23: 5 residues within 4Å:- Chain A: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIPCL.44: 3 residues within 4Å:- Chain B: R.56, C.160, N.163
Ligand excluded by PLIPCL.45: 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: 5 residues within 4Å:- Chain D: R.67, Y.173, A.457, P.458, H.584
Ligand excluded by PLIP- 1 x PEG: DI(HYDROXYETHYL)ETHER(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
IB
JC
KD
L
- 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)
- 26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 4 x SRM: SIROHEME(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(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 PEG: DI(HYDROXYETHYL)ETHER(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
IB
JC
KD
L