- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.41 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x TP7: Coenzyme B
TP7.2: 20 residues within 4Å:- Chain A: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482
- Chain B: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381
- Chain D: R.225, K.256, H.257
22 PLIP interactions:5 interactions with chain A, 10 interactions with chain B, 7 interactions with chain D- Hydrophobic interactions: A:M.324, A:F.330, B:F.362, B:F.362, B:Y.367, B:Y.367, B:I.380, B:V.381
- Water bridges: A:R.270, A:M.324, B:Y.367, B:G.369, D:R.225, D:R.225
- Salt bridges: A:R.270, B:H.379, D:R.225, D:K.256, D:K.256
- Hydrogen bonds: B:G.369, D:K.256, D:K.256
TP7.23: 20 residues within 4Å:- Chain A: R.225, K.256, H.257
- Chain D: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482
- Chain E: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381
22 PLIP interactions:9 interactions with chain E, 8 interactions with chain A, 5 interactions with chain D- Hydrophobic interactions: E:F.362, E:F.362, E:Y.367, E:Y.367, E:I.380, E:V.381, D:M.324, D:F.330
- Hydrogen bonds: E:G.369, A:K.256, A:K.256
- Water bridges: E:G.369, A:R.225, A:R.225, A:K.256, D:R.270, D:M.324
- Salt bridges: E:H.379, A:R.225, A:K.256, A:K.256, D:R.270
- 5 x K: POTASSIUM ION(Non-covalent)
K.3: 8 residues within 4Å:- Chain A: R.102, S.215, R.216, C.218
- Chain D: R.102, S.215, R.216, C.218
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain D- Metal complexes: A:R.216, A:C.218, D:R.216, D:C.218
K.8: 1 residues within 4Å:- Chain A: D.170
5 PLIP interactions:1 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.170, H2O.6, H2O.11, H2O.11, H2O.12
K.21: 2 residues within 4Å:- Chain C: S.51, A.78
5 PLIP interactions:2 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:S.51, C:A.78, H2O.44, H2O.44, H2O.46
K.30: 3 residues within 4Å:- Chain D: E.117, V.124
- Ligands: ETX.33
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:V.124, H2O.58, H2O.58, H2O.58, H2O.69
K.36: 1 residues within 4Å:- Chain E: K.7
4 PLIP interactions:1 interactions with chain E, 3 Ligand-Water interactions- Metal complexes: E:K.7, H2O.70, H2O.70, H2O.80
- 12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)
CA.4: 2 residues within 4Å:- Chain A: E.190, E.194
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.190, A:E.194, H2O.12, H2O.12, H2O.12
CA.5: 4 residues within 4Å:- Chain A: P.58, I.60, G.61, T.62
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:P.58, A:I.60, H2O.5, H2O.6, H2O.6
CA.6: 2 residues within 4Å:- Chain A: K.11, F.14
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:K.11, A:F.14, H2O.1, H2O.2, H2O.2
CA.7: 1 residues within 4Å:- Chain A: D.174
5 PLIP interactions:5 Ligand-Water interactions- Metal complexes: H2O.11, H2O.11, H2O.11, H2O.11, H2O.23
CA.15: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)CA.25: 2 residues within 4Å:- Chain D: K.11, F.14
5 PLIP interactions:2 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:K.11, D:F.14, H2O.52, H2O.52, H2O.53
CA.26: 4 residues within 4Å:- Chain D: P.58, I.60, G.61, T.62
5 PLIP interactions:2 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:P.58, D:I.60, H2O.10, H2O.10, H2O.56
CA.27: 1 residues within 4Å:- Chain D: D.170
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:D.170, H2O.60, H2O.60, H2O.60, H2O.69
CA.28: 1 residues within 4Å:- Chain D: D.174
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:D.174, H2O.60, H2O.60, H2O.60, H2O.61
CA.29: 2 residues within 4Å:- Chain D: E.190, E.194
5 PLIP interactions:2 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:E.190, D:E.194, H2O.61, H2O.61, H2O.61
CA.35: 1 residues within 4Å:- Chain E: D.271
5 PLIP interactions:1 interactions with chain E, 4 Ligand-Water interactions- Metal complexes: E:D.271, H2O.81, H2O.81, H2O.81, H2O.81
CA.46: 2 residues within 4Å:- Chain F: S.51, A.78
5 PLIP interactions:2 interactions with chain F, 3 Ligand-Water interactions- Metal complexes: F:S.51, F:A.78, H2O.89, H2O.89, H2O.90
- 2 x F43: FACTOR 430(Non-covalent)
F43.9: 34 residues within 4Å:- Chain A: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443
- Chain B: S.365, I.366, Y.367
- Chain C: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158
- Chain D: A.144, V.145, V.146, Q.147, M.150, Q.230, M.233, I.236, A.243
- Ligands: COM.1
37 PLIP interactions:8 interactions with chain D, 2 interactions with chain B, 12 interactions with chain A, 15 interactions with chain C,- Hydrophobic interactions: D:Q.147, D:I.236, D:A.243, A:V.328, A:F.330, A:Y.333, A:Y.333, A:F.396, A:F.443, C:L.117
- Hydrogen bonds: D:V.145, D:V.146, D:Q.147, D:Q.230, B:I.366, B:Y.367, A:V.328, A:G.329, A:Q.332, A:Q.332, A:Y.333, C:S.118, C:G.119, C:R.120, C:S.154, C:V.155, C:G.157
- Water bridges: D:A.243, A:T.331, C:S.118, C:S.118, C:G.152, C:H.156, C:H.158, C:H.158
- Salt bridges: C:H.156, C:H.158
F43.31: 34 residues within 4Å:- Chain A: A.144, V.145, V.146, Q.147, M.150, Q.230, M.233, I.236, A.243
- Chain D: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443
- Chain E: S.365, I.366, Y.367
- Chain F: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158
- Ligands: COM.24
40 PLIP interactions:16 interactions with chain F, 13 interactions with chain D, 8 interactions with chain A, 3 interactions with chain E,- Hydrophobic interactions: F:L.117, D:V.328, D:F.330, D:Y.333, D:Y.333, D:F.396, D:F.443, A:Q.147, A:I.236, A:A.243
- Hydrogen bonds: F:S.118, F:G.119, F:R.120, F:S.154, F:V.155, F:G.157, D:V.328, D:G.329, D:Q.332, D:Q.332, D:Y.333, D:Y.333, A:V.145, A:V.146, A:Q.147, A:Q.230, E:I.366, E:Y.367, E:Y.367
- Water bridges: F:S.118, F:S.118, F:G.152, F:H.156, F:H.158, F:H.158, F:H.158, D:T.331, A:A.243
- Salt bridges: F:H.156, F:H.158
- 26 x ETX: 2-ETHOXYETHANOL(Non-covalent)
ETX.10: 9 residues within 4Å:- Chain A: F.513, D.515, D.516, L.518, V.519, F.520, D.521, F.522
- Ligands: ETX.14
Ligand excluded by PLIPETX.11: 1 residues within 4Å:- Chain A: D.368
Ligand excluded by PLIPETX.12: 5 residues within 4Å:- Chain A: D.345, Y.348, F.349, E.352, Y.380
Ligand excluded by PLIPETX.13: 2 residues within 4Å:- Chain A: D.356, K.357
Ligand excluded by PLIPETX.14: 8 residues within 4Å:- Chain A: V.519, D.521, E.528, K.531, E.536, F.537, E.538
- Ligands: ETX.10
Ligand excluded by PLIPETX.16: 8 residues within 4Å:- Chain B: Q.40, K.43, S.118, F.121, D.122
- Chain E: F.121, D.122
- Ligands: ETX.37
Ligand excluded by PLIPETX.17: 7 residues within 4Å:- Chain B: G.402, T.403, Q.404, M.405
- Chain C: V.52
- Chain D: K.118, R.119
Ligand excluded by PLIPETX.18: 5 residues within 4Å:- Chain B: K.61, A.66, K.68
- Chain D: E.199, P.507
Ligand excluded by PLIPETX.19: 5 residues within 4Å:- Chain B: E.83, A.86, A.87, K.90, V.103
Ligand excluded by PLIPETX.20: 6 residues within 4Å:- Chain B: K.7, V.8, D.9, Q.21, Y.243, D.249
Ligand excluded by PLIPETX.22: 4 residues within 4Å:- Chain C: E.232, Q.235, R.236, V.239
Ligand excluded by PLIPETX.32: 8 residues within 4Å:- Chain D: F.513, D.515, D.516, L.518, V.519, F.520, D.521, F.522
Ligand excluded by PLIPETX.33: 5 residues within 4Å:- Chain D: H.113, V.124, T.125, P.126
- Ligands: K.30
Ligand excluded by PLIPETX.34: 7 residues within 4Å:- Chain B: P.65
- Chain D: W.205, H.257, A.258, E.259, V.260, I.261
Ligand excluded by PLIPETX.37: 8 residues within 4Å:- Chain B: D.122
- Chain E: Q.40, K.43, S.118, F.121, D.122
- Ligands: ETX.16, ETX.44
Ligand excluded by PLIPETX.38: 1 residues within 4Å:- Chain E: E.83
Ligand excluded by PLIPETX.39: 3 residues within 4Å:- Chain E: D.12, N.16, L.17
Ligand excluded by PLIPETX.40: 7 residues within 4Å:- Chain A: K.118, R.119
- Chain E: G.402, T.403, Q.404, M.405
- Chain F: V.52
Ligand excluded by PLIPETX.41: 5 residues within 4Å:- Chain A: E.199, W.205, P.507
- Chain E: K.61, A.66
Ligand excluded by PLIPETX.42: 5 residues within 4Å:- Chain E: L.205, K.416, S.420, Q.421, R.426
Ligand excluded by PLIPETX.43: 6 residues within 4Å:- Chain E: L.251, D.254, L.255, A.258, D.271, R.275
Ligand excluded by PLIPETX.44: 4 residues within 4Å:- Chain E: S.118, A.119, D.122
- Ligands: ETX.37
Ligand excluded by PLIPETX.45: 7 residues within 4Å:- Chain A: I.460
- Chain B: A.232, F.233
- Chain C: Y.246, N.247
- Chain E: Q.140, N.144
Ligand excluded by PLIPETX.48: 3 residues within 4Å:- Chain E: F.4, R.235
- Chain F: E.249
Ligand excluded by PLIPETX.49: 7 residues within 4Å:- Chain B: Q.140, I.143, N.144
- Chain E: A.232, F.233
- Chain F: Y.246, N.247
Ligand excluded by PLIPETX.50: 4 residues within 4Å:- Chain F: E.232, Q.235, R.236, V.239
Ligand excluded by PLIP- 1 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagner, T. et al., Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. (2016)
- Release Date
- 2016-08-03
- Peptides
- METHYL-COENZYME M REDUCTASE: AD
METHYL-COENZYME M REDUCTASE: BE
METHYL-COENZYME M REDUCTASE: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.41 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x TP7: Coenzyme B
- 5 x K: POTASSIUM ION(Non-covalent)
- 12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)
- 2 x F43: FACTOR 430(Non-covalent)
- 26 x ETX: 2-ETHOXYETHANOL(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wagner, T. et al., Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. (2016)
- Release Date
- 2016-08-03
- Peptides
- METHYL-COENZYME M REDUCTASE: AD
METHYL-COENZYME M REDUCTASE: BE
METHYL-COENZYME M REDUCTASE: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F