SMTL ID : 7z7i.1

Structure of ADP-ribosylated F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308, K.338 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:D.159, A:D.159, A:D.159, A:K.215, A:E.216, A:G.304 Salt bridges: A:K.20, A:K.20 ADP.4: 14 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308, K.338 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:E.216, B:G.304 Salt bridges: B:K.20, B:K.20 ADP.7: 14 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308, K.338 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:D.159, C:D.159, C:D.159, C:K.215, C:E.216, C:G.304 Salt bridges: C:K.20, C:K.20 ADP.10: 14 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308, K.338 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:E.216, D:G.304 Salt bridges: D:K.20, D:K.20 ADP.13: 14 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308, K.338 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.16, E:G.17, E:L.18, E:D.159, E:D.159, E:D.159, E:K.215, E:E.216, E:G.304 Salt bridges: E:K.20, E:K.20

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: ADP.13 No protein-ligand interaction detected (PLIP)

5 x APR: ADENOSINE-5-DIPHOSPHORIBOSE(Covalent)

APR.3: 7 residues within 4Å: Chain A: T.150, T.151, E.169 Chain B: K.52, D.58, E.59, S.62 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.52, B:K.52, B:D.58, B:S.62, B:S.62, A:T.151, A:E.169, A:E.169 APR.6: 3 residues within 4Å: Chain B: T.150, T.151, E.169 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.151, B:E.169, B:E.169 APR.9: 7 residues within 4Å: Chain C: T.150, T.151, E.169 Chain D: K.52, D.58, E.59, S.62 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.52, D:K.52, D:D.58, D:S.62, D:S.62, C:T.151, C:E.169, C:E.169 APR.12: 7 residues within 4Å: Chain D: T.150, T.151, E.169 Chain E: K.52, D.58, E.59, S.62 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:K.52, E:K.52, E:D.58, E:E.59, E:S.62, E:S.62, D:T.151, D:E.169, D:E.169 APR.15: 3 residues within 4Å: Chain E: T.150, T.151, E.169 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.151, E:E.169, E:E.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Belyy, A. et al., Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Commun (2022)

Release Date

2022-06-29

Peptides

Actin, alpha skeletal muscle: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
E

D
C

E
A

Actin, alpha skeletal muscle

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