SMTL ID : 6bxm.1

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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, G.162, C.163, Q.241, C.287, R.289 Ligands: SAM.2 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.65, A:C.163, A:C.287 SF4.3: 10 residues within 4Å: Chain B: F.62, C.65, R.153, G.162, C.163, Q.241, C.287, R.289 Ligands: ABA.4, MTA.5 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.65, B:C.163, B:C.287

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.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 12 PLIP interactions: 12 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:V.160, A:R.289 Salt bridges: A:H.184, A:R.289 pi-Stacking: A:F.62

1 x ABA: ALPHA-AMINOBUTYRIC ACID(Non-functional Binders)

ABA.4: 7 residues within 4Å: Chain B: F.62, L.161, G.162, H.184, R.289 Ligands: SF4.3, MTA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.162 Salt bridges: B:H.184, B:R.289

1 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.5: 14 residues within 4Å: Chain B: F.62, 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, ABA.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.236, B:Q.241, B:D.267, B:V.269, B:D.293, B:D.293, B:D.294 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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