SMTL ID : 8cnr.1

Hybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus as isolated in a reduced state at 1.45-A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: S.188, L.189 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.188, H2O.19 MG.2: 3 residues within 4Å: Chain A: E.299, S.318, R.322 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.299, H2O.11 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: K.214 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 10 residues within 4Å: Chain A: Y.9, E.140, R.143, S.144, A.516, F.517, L.518, S.519 Ligands: GOL.11, GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.9 Hydrogen bonds: A:E.140 Salt bridges: A:R.143

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 12 residues within 4Å: Chain A: M.6, C.8, Y.9, Q.10, C.11, T.14, C.20, G.24, V.25, C.26, K.28, T.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.8, A:C.11, A:C.20, A:C.26

1 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.7: 3 residues within 4Å: Chain A: K.256, K.279, Y.280 No protein-ligand interaction detected (PLIP)

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.8: 1 residues within 4Å: Chain A: T.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.195 FMT.10: 3 residues within 4Å: Chain A: D.172, K.203, Y.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.172, A:D.172, A:K.203, A:Y.204 FMT.12: 2 residues within 4Å: Chain A: V.206, Y.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.459

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: T.219, Y.220, G.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.220 Water bridges: A:G.221

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: T.18, E.140, A.516, L.518, S.519, P.520 Ligands: ACT.3, GOL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.140 Water bridges: A:L.518 GOL.13: 3 residues within 4Å: Chain A: E.94, A.117, D.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:E.94, A:E.94, A:A.117 GOL.16: 6 residues within 4Å: Chain A: F.7, Y.9, T.18, R.143 Ligands: ACT.3, GOL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.18, A:R.143

1 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.14: 11 residues within 4Å: Chain A: H.243, E.267, W.291, N.310, C.311, C.402, D.403, C.430, C.455, Y.489, E.490 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Water interactions, Salt bridges: A:E.267, A:E.490, A:E.490 Metal complexes: A:H.243, A:E.267, A:C.311, A:C.402, A:C.430, A:C.455, A:E.490, H2O.1

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.15: 8 residues within 4Å: Chain A: L.145, T.195, V.198, L.199, V.522, V.525, L.526, F.530 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.145, A:T.195, A:V.198, A:L.199, A:V.522, A:L.526, A:L.526, A:F.530, A:F.530

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 the thermophilic methanogen Methanothermococcus thermolithotrophicus: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hybrid cluster protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus

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