SMTL ID : 7z7h.1

Structure of P. luminescens TccC3-F-actin complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-1-mer

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.303, G.304, Y.308, K.338 Ligands: MG.2 12 PLIP interactions: 12 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:E.216, A:G.304 Salt bridges: A:K.20, A:K.20 ADP.5: 14 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, D.159, K.215, E.216, G.303, G.304, M.307, Y.308, K.338 Ligands: MG.6 12 PLIP interactions: 12 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:E.216, C:G.304 Salt bridges: C:K.20, C:K.20 ADP.7: 12 residues within 4Å: Chain D: S.16, G.17, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308 Ligands: MG.8 10 PLIP interactions: 10 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:G.304 Salt bridges: D:K.20, D:K.20 ADP.9: 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.303, G.304, M.307, Y.308 Ligands: MG.10 12 PLIP interactions: 12 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:E.216, E:G.304 Salt bridges: E:K.20, E:K.20 ADP.11: 12 residues within 4Å: Chain F: G.15, S.16, L.18, K.20, G.158, D.159, K.215, E.216, G.304, M.307, Y.308 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.16, F:G.17, F:L.18, F:D.159, F:D.159, F:D.159, F:K.215, F:E.216, F:G.304 Salt bridges: F:K.20, F:K.20

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

MG.2: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: K.20 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: G.158 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

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

APR.3: 10 residues within 4Å: Chain A: T.150 Chain B: R.409, N.412, R.413, K.427, W.429, K.478, K.481, G.497 Ligands: NCA.4 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.409, B:R.409, B:N.412, B:N.412, B:R.413, B:R.413, B:K.427, A:T.150 Salt bridges: B:K.481, B:K.481 pi-Cation interactions: B:R.413, B:R.413

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.4: 8 residues within 4Å: Chain B: Y.408, R.409, A.410, S.489, T.490, A.491, A.496 Ligands: APR.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.491, B:A.496 Hydrogen bonds: B:R.409, B:A.410, B:A.410

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: ACDEF
Maltose/maltodextrin-binding periplasmic protein,TccC3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
B

D
E

E
C

F
A

B
F

Actin, alpha skeletal muscle

Maltose/maltodextrin-binding periplasmic protein,TccC3

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