- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- monomer
- Ligands
- 4 x HOA: HYDROXYAMINE(Non-functional Binders)(Non-covalent)
- 10 x FMT: FORMIC ACID(Non-functional Binders)
FMT.3: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)FMT.20: 3 residues within 4Å:- Chain A: Y.9, R.143
- Ligands: TRS.21
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.9, A:Y.9, A:R.143
FMT.22: 4 residues within 4Å:- Chain A: D.507, E.528, K.529, G.531
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.528
FMT.23: 2 residues within 4Å:- Chain A: A.191, N.521
1 PLIP interactions:1 interactions with chain A- Water bridges: A:T.195
FMT.24: 4 residues within 4Å:- Chain A: E.352, Q.353, K.356
- Ligands: EDO.14
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.353, A:K.356
- Water bridges: A:Q.353
FMT.28: 6 residues within 4Å:- Chain A: R.2, S.4, K.5, N.34, N.128
- Ligands: EDO.10
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.34
FMT.30: 2 residues within 4Å:- Chain A: D.172, Y.204
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.204
- Water bridges: A:K.203, A:D.207
FMT.31: 5 residues within 4Å:- Chain A: L.514, P.515, L.518, A.523
- Ligands: TRS.21
2 PLIP interactions:2 interactions with chain A- Water bridges: A:N.17, A:N.17
FMT.34: 2 residues within 4Å:- Chain A: T.536, E.540
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.540
FMT.36: 4 residues within 4Å:- Chain A: V.25, C.26, G.27, R.405
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.25
- Water bridges: A:G.27
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x SF3: FE4-S3 CLUSTER(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 6 residues within 4Å:- Chain A: D.58, M.164, G.167, Y.168, D.169, K.171
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.58, A:M.164, A:D.169, A:K.171
EDO.9: 5 residues within 4Å:- Chain A: D.37, V.40, Y.41, K.44, V.132
6 PLIP interactions:6 interactions with chain A- Water bridges: A:K.44, A:K.44, A:K.44, A:E.147, A:E.147, A:T.184
EDO.10: 6 residues within 4Å:- Chain A: K.5, D.30, N.31, N.34, N.128
- Ligands: FMT.28
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.34, A:N.128
- Water bridges: A:N.31
EDO.11: 5 residues within 4Å:- Chain A: D.229, G.231, V.232, R.233, V.284
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:D.229, A:V.232, A:R.233
- Water bridges: A:D.229, A:G.231, A:R.233
EDO.12: 3 residues within 4Å:- Chain A: K.389, V.471, F.472
No protein-ligand interaction detected (PLIP)EDO.13: 4 residues within 4Å:- Chain A: I.368, V.369, N.436, V.449
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:V.369
- Water bridges: A:N.436, A:D.451, A:D.451
EDO.14: 4 residues within 4Å:- Chain A: D.321, Q.353, C.357
- Ligands: FMT.24
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.353
- Water bridges: A:D.321, A:R.322
EDO.16: 6 residues within 4Å:- Chain A: K.320, D.321, I.323, Y.324, L.334, K.335
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:I.323, A:K.335
EDO.17: 3 residues within 4Å:- Chain A: S.348, I.351, E.352
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.348
- Water bridges: A:K.355
EDO.18: 3 residues within 4Å:- Chain A: A.210, L.211, K.214
No protein-ligand interaction detected (PLIP)- 1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 1 x VQ8: hybrid cluster(Non-covalent)
- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.26: 5 residues within 4Å:- Chain A: G.27, K.29, F.77, F.331, P.332
3 PLIP interactions:3 interactions with chain A- Water bridges: A:F.77, A:D.79
- Salt bridges: A:K.29
ACT.27: 3 residues within 4Å:- Chain A: A.136, R.146, D.187
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.146
ACT.29: 5 residues within 4Å:- Chain A: K.417, K.418, L.419, P.420, N.421
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.421
ACT.32: 4 residues within 4Å:- Chain A: V.165, L.166, G.167, K.246
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.246
- 1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lemaire, O.N. et al., Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front Microbiol (2023)
- Release Date
- 2023-04-19
- Peptides
- Hybrid cluster protein from Methanothermococcus thermolithotrophicus: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- monomer
- Ligands
- 4 x HOA: HYDROXYAMINE(Non-functional Binders)(Non-covalent)
- 10 x FMT: FORMIC ACID(Non-functional Binders)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x SF3: FE4-S3 CLUSTER(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 1 x VQ8: hybrid cluster(Non-covalent)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lemaire, O.N. et al., Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front Microbiol (2023)
- Release Date
- 2023-04-19
- Peptides
- Hybrid cluster protein from Methanothermococcus thermolithotrophicus: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A