SMTL ID : 6bxl.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 15 residues within 4Å: Chain A: Y.92, L.197, G.198, H.220, S.272, K.274, Q.277, N.303, D.304, V.305, C.323, R.325, V.326, D.329 Ligands: SF4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.198, A:S.272, A:Q.277, A:N.303, A:D.304, A:V.305, A:R.325, A:D.329 Salt bridges: A:H.220 SAM.3: 15 residues within 4Å: Chain B: Y.92, L.197, G.198, H.220, S.272, K.274, Q.277, N.303, D.304, V.305, C.323, R.325, V.326, D.329 Ligands: SF4.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.198, B:S.272, B:Q.277, B:Q.277, B:V.305, B:R.325, B:D.329 Salt bridges: B:H.220, B:R.325

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

SF4.2: 8 residues within 4Å: Chain A: Y.92, C.95, L.197, G.198, C.199, Q.277, C.323 Ligands: SAM.1 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.95, A:C.199, A:C.323 SF4.4: 10 residues within 4Å: Chain B: Y.92, C.95, R.189, L.197, G.198, C.199, Q.277, C.323, R.325 Ligands: SAM.3 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.95, B:C.199, B:C.323

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

2-(3-amino-3-carboxypropyl)histidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-(3-amino-3-carboxypropyl)histidine synthase

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