SMTL ID : 6q2e.1

Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

MTA.1: 13 residues within 4Å: Chain A: F.61, S.240, K.242, Q.245, D.271, N.272, I.273, C.292, R.294, I.295, D.298, D.299 Ligands: SF4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.240, A:Q.245, A:Q.245, A:I.273, A:D.298, A:D.299 Water bridges: A:R.294 pi-Stacking: A:F.61 MTA.4: 13 residues within 4Å: Chain B: F.61, S.240, K.242, Q.245, D.271, N.272, I.273, C.292, R.294, I.295, D.298, D.299 Ligands: SF4.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.240, B:Q.245, B:Q.245, B:I.273, B:D.298, B:D.298, B:D.299 pi-Stacking: B:F.61

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

SF4.2: 9 residues within 4Å: Chain A: F.61, C.64, G.163, C.164, Q.245, C.292, P.293, R.294 Ligands: MTA.1 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.64, A:C.164, A:C.292 SF4.5: 7 residues within 4Å: Chain B: F.61, C.64, G.163, C.164, C.292, R.294 Ligands: MTA.4 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.64, B:C.164, B:C.292

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: Y.246, R.247, M.248, K.249 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis. Biochemistry (2019)

Release Date

2019-10-16

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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