SMTL ID : 9b27.1

Dia1 at the Barbed End of F-Actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.51 Å

Oligo State

hetero-6-2-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: G.9, S.10, G.11, L.12, K.14, G.152, D.153, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.10, A:G.11, A:L.12, A:D.153, A:D.153, A:D.153, A:K.209, A:K.209, A:G.298, A:K.332, A:K.332 Salt bridges: A:K.14, A:K.14 ADP.3: 16 residues within 4Å: Chain B: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:L.12, B:D.153, B:D.153, B:K.209, B:E.210, B:G.298, B:K.332, B:K.332 Salt bridges: B:K.14, B:K.14 ADP.5: 16 residues within 4Å: Chain C: D.7, G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, K.209, E.210, G.298, T.299, Y.302, K.332 Ligands: MG.6 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:D.153, C:K.209, C:K.332 Salt bridges: C:K.14, C:K.14 ADP.7: 14 residues within 4Å: Chain D: G.9, S.10, G.11, L.12, K.14, G.152, D.153, K.209, E.210, G.298, T.299, Y.302, K.332 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.10, D:G.11, D:L.12, D:L.12, D:D.153, D:D.153, D:K.209, D:G.298, D:K.332, D:K.332 Salt bridges: D:K.14, D:K.14 ADP.9: 16 residues within 4Å: Chain E: G.9, S.10, G.11, L.12, K.14, G.152, D.153, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.10, E:G.11, E:L.12, E:L.12, E:D.153, E:D.153, E:K.209, E:G.298, E:K.332, E:K.332 Salt bridges: E:K.14, E:K.14 pi-Stacking: E:Y.302 ADP.11: 17 residues within 4Å: Chain F: D.7, 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 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.10, F:G.11, F:L.12, F:D.153, F:K.209, F:E.210, F:G.298, F:M.301 Salt bridges: F:K.14, F:K.14 pi-Stacking: F:Y.302

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: G.152, D.153 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: G.152 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: D.7, Q.133 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.7 MG.8: 3 residues within 4Å: Chain D: G.152, D.153 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: G.152, D.153 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: D.7, G.9, Q.133 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palmer, N.J. et al., Mechanisms of actin filament severing and elongation by formins. Nature (2024)

Release Date

2024-05-29

Peptides

Actin, alpha skeletal muscle: ABCDEF
Protein diaphanous homolog 1: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Actin, alpha skeletal muscle

Protein diaphanous homolog 1

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