SMTL ID : 9jus.1 (1 other biounit)

Structure of villin bound to an actin trimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:L.18, A:D.159, A:D.159, A:K.215, A:E.216, A:E.216, A:G.304, A:T.305 Water bridges: A:G.184, A:T.188 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.3: 18 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:D.159, B:D.159, B:K.215, B:G.304, B:M.307, B:K.338 Water bridges: B:D.13, B:K.20, B:Y.308 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.5: 18 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:L.18, C:D.159, C:D.159, C:D.159, C:R.212, C:K.215, C:E.216, C:G.304, C:K.338 Water bridges: C:K.20 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308

3 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.4: 3 residues within 4Å: Chain B: D.13, K.20 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.156 Ligands: ADP.5 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain D: G.39, D.40, E.70, V.119 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:G.39, D:D.40, D:E.70, D:V.119, H2O.5 CA.8: 4 residues within 4Å: Chain B: E.169 Chain D: D.82, G.87, P.89 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.82, D:P.89, B:E.169, H2O.2, H2O.2 CA.9: 4 residues within 4Å: Chain D: G.159, D.160, E.182, D.245 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.160, D:E.182, D:E.182, D:D.245, H2O.3 CA.10: 3 residues within 4Å: Chain D: N.286, D.287, E.310 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:N.286, D:E.310, D:E.310, H2O.4, H2O.4 CA.11: 4 residues within 4Å: Chain D: G.426, D.427, E.457, K.505 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.427, D:E.457, D:K.505, H2O.4, H2O.4 CA.12: 5 residues within 4Å: Chain A: E.169 Chain D: D.469, G.474, T.475, A.476 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.469, D:D.469, D:G.474, D:A.476, H2O.1 CA.13: 3 residues within 4Å: Chain D: N.548, D.549, E.571 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:N.548, D:D.549, D:E.571, D:E.571, H2O.3 CA.14: 5 residues within 4Å: Chain A: D.313 Chain D: S.630, E.652, D.653, E.675 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.653, D:E.675, D:E.675, H2O.1, H2O.1

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

CL.15: 4 residues within 4Å: Chain B: P.334, E.336, S.340 Chain D: Q.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, R.C., The structure of a villin-stabilized actin nucleus. To Be Published

Release Date

2025-10-08

Peptides

Actin, alpha skeletal muscle: ABC
villin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
p

B
f

C
g

D
v

Actin, alpha skeletal muscle

villin

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