SMTL ID : 8d16.1

Bent ADP-Pi-F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.2, PO4.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.10, A:G.11, A:L.12, A:L.12, A:D.153, A:D.153, A:K.209, A:E.210, A:G.298, A:T.299 Salt bridges: A:K.14, A:K.14 ADP.4: 19 residues within 4Å: Chain B: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.5, PO4.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:L.12, B:L.12, B:D.153, B:D.153, B:K.209, B:G.298, B:K.332 Salt bridges: B:K.14, B:K.14 pi-Stacking: B:Y.302 ADP.7: 17 residues within 4Å: Chain C: G.9, S.10, G.11, L.12, K.14, G.152, D.153, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.8, PO4.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.10, C:G.11, C:L.12, C:D.153, C:D.153, C:K.209, C:G.298, C:T.299 Salt bridges: C:K.14, C:K.14 ADP.10: 18 residues within 4Å: Chain D: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.11, PO4.12 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.10, D:S.10, D:G.11, D:L.12, D:D.153, D:D.153, D:K.209, D:G.298, D:T.299, D:M.301, D:K.332 Salt bridges: D:K.14, D:K.14 pi-Stacking: D:Y.302 ADP.13: 17 residues within 4Å: Chain E: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, K.209, E.210, G.297, G.298, T.299, M.301, Y.302 Ligands: MG.14, PO4.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.10, E:S.10, E:G.11, E:L.12, E:D.153, E:D.153, E:K.209, E:E.210, E:E.210, E:G.298, E:T.299 Salt bridges: E:K.14, E:K.14 ADP.16: 19 residues within 4Å: Chain F: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, R.206, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.17, PO4.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:S.10, F:G.11, F:L.12, F:D.153, F:D.153, F:K.209, F:E.210, F:G.298, F:K.332 Salt bridges: F:K.14, F:K.14 pi-Stacking: F:Y.302 ADP.19: 17 residues within 4Å: Chain G: G.9, S.10, G.11, L.12, K.14, G.152, D.153, K.209, E.210, G.297, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.20, PO4.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.10, G:G.11, G:L.12, G:D.153, G:D.153, G:D.153, G:K.209, G:E.210, G:G.298, G:K.332 Salt bridges: G:K.14, G:K.14

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.133, D.150, G.152 Ligands: ADP.1, PO4.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.133 Ligands: ADP.4, PO4.6 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: Q.133, D.150, G.152 Ligands: ADP.7, PO4.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: Q.133, D.150 Ligands: ADP.10, PO4.12 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain E: Q.133 Ligands: ADP.13, PO4.15 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain F: D.7, Q.133 Ligands: ADP.16, PO4.18 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain G: D.150, G.297 Ligands: ADP.19, PO4.21 No protein-ligand interaction detected (PLIP)

7 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: S.10, Q.133, G.152, D.153, G.154, V.155 Ligands: ADP.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.10, A:S.10, A:Q.133, A:D.153, A:G.154, A:V.155, A:V.155 PO4.6: 9 residues within 4Å: Chain B: S.10, G.70, Q.133, G.152, D.153, G.154, V.155 Ligands: ADP.4, MG.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.10, B:Q.133, B:G.152, B:D.153, B:G.154, B:V.155, B:V.155 PO4.9: 10 residues within 4Å: Chain C: G.9, S.10, G.70, Q.133, G.152, D.153, G.154, V.155 Ligands: ADP.7, MG.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.10, C:S.10, C:Q.133, C:G.152, C:D.153, C:G.154, C:V.155 PO4.12: 8 residues within 4Å: Chain D: S.10, Q.133, G.152, D.153, G.154, V.155 Ligands: ADP.10, MG.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.10, D:Q.133, D:G.152, D:D.153, D:G.154, D:V.155, D:V.155 PO4.15: 7 residues within 4Å: Chain E: S.10, Q.133, D.153, G.154, V.155 Ligands: ADP.13, MG.14 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.10, E:S.10, E:Q.133, E:D.153, E:G.154, E:V.155, E:V.155 PO4.18: 8 residues within 4Å: Chain F: S.10, Q.133, G.152, D.153, G.154, V.155 Ligands: ADP.16, MG.17 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.10, F:Q.133, F:G.152, F:D.153, F:G.154, F:V.155, F:V.155 PO4.21: 10 residues within 4Å: Chain G: S.10, A.104, Q.133, D.150, G.152, D.153, G.154, V.155 Ligands: ADP.19, MG.20 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:S.10, G:Q.133, G:G.152, G:D.153, G:G.154, G:V.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reynolds, M.J. et al., Bending forces and nucleotide state jointly regulate F-actin structure. Nature (2022)

Release Date

2022-09-07

Peptides

Actin, alpha skeletal muscle, intermediate form: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Actin, alpha skeletal muscle, intermediate form

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