SMTL ID : 6bxo.1

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 8 residues within 4Å: Chain A: F.62, C.65, R.153, G.162, C.163, Q.241, C.287 Ligands: SAH.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.65, A:C.163, A:C.287, SAH.2 SF4.3: 8 residues within 4Å: Chain B: F.62, C.65, R.153, G.162, C.163, C.287, R.289 Ligands: SAH.4 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.65, B:C.163, B:C.287

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 16 residues within 4Å: Chain A: F.62, L.161, G.162, H.184, S.236, K.238, Q.241, D.267, L.268, V.269, C.287, R.289, I.290, D.293, D.294 Ligands: SF4.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.162, A:S.236, A:Q.241, A:Q.241, A:V.269, A:D.293, A:D.294 Water bridges: A:R.289, A:D.293 Salt bridges: A:H.184 pi-Stacking: A:F.62 SAH.4: 16 residues within 4Å: Chain B: F.62, L.161, G.162, H.184, S.236, K.238, Q.241, D.267, L.268, V.269, C.287, R.289, I.290, D.293, D.294 Ligands: SF4.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.162, B:S.236, B:Q.241, B:D.267, B:V.269, B:D.293, B:D.293, B:D.294 Salt bridges: B:H.184 pi-Stacking: B:F.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, M. et al., Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Science (2018)

Release Date

2018-04-11

Peptides

Diphthamide biosynthesis enzyme Dph2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diphthamide biosynthesis enzyme Dph2

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