SMTL ID : 8smd.1

Structure of Clostridium botulinum prophage Tad1 in complex with 1''-3' gcADPR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x OJC: (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione(Non-covalent)

OJC.1: 19 residues within 4Å: Chain A: P.25, G.26, H.30, Q.54, K.55, G.56, A.57, R.58, R.110, R.114, L.120, G.121, T.122, N.123 Chain B: R.79, L.80, F.83, F.88, N.93 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.79, B:R.79, B:N.93, B:N.93, A:H.30, A:G.56, A:R.58, A:R.110, A:G.121 pi-Stacking: B:F.83, B:F.83 Salt bridges: A:R.58, A:R.110, A:R.114 pi-Cation interactions: A:R.110, A:R.110 OJC.2: 19 residues within 4Å: Chain A: R.79, L.80, F.83, F.88, N.93 Chain B: P.25, G.26, H.30, Q.54, K.55, G.56, A.57, R.58, R.110, R.114, L.120, G.121, T.122, N.123 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.30, B:G.56, B:R.58, B:R.110, B:R.110, B:G.121, A:R.79, A:R.79, A:N.93, A:N.93 Salt bridges: B:R.58, B:R.110, B:R.114 pi-Cation interactions: B:R.110, B:R.110 pi-Stacking: A:F.83, A:F.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yirmiya, E. et al., Phages overcome bacterial immunity via diverse anti-defence proteins. Nature (2024)

Release Date

2023-11-22

Peptides

ABC transporter ATPase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ABC transporter ATPase

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