SMTL ID : 3lzd.1

Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: Y.92, C.95, R.189, G.198, C.199, Q.277, C.323, I.359 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.95, A:C.199, A:C.323 SF4.3: 8 residues within 4Å: Chain B: Y.92, C.95, M.118, R.189, G.198, C.199, C.323 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.95, B:C.199, B:C.323

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: L.197, G.198, H.220, R.325 Ligands: SF4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.198 Salt bridges: A:H.220, A:R.325 SO4.4: 5 residues within 4Å: Chain B: L.197, G.198, H.220, R.325 Ligands: SF4.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.198 Water bridges: B:R.325 Salt bridges: B:H.220, B:R.325 SO4.5: 3 residues within 4Å: Chain B: G.184, R.185, V.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.185 Water bridges: B:R.185, B:G.186, B:V.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature (2010)

Release Date

2010-07-14

Peptides

Dph2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dph2

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