SMTL ID : 6vec.1

Cryo-EM structure of F-actin/Plastin2-ABD2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-11-11-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.13, A:S.16, A:D.159, A:D.159, A:D.159, A:K.215, A:G.304, A:K.338 pi-Stacking: A:Y.308 ADP.3: 15 residues within 4Å: Chain B: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.13, B:S.16, B:D.159, B:D.159, B:D.159, B:K.215, B:G.304, B:K.338 pi-Stacking: B:Y.308 ADP.5: 15 residues within 4Å: Chain C: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.13, C:S.16, C:D.159, C:D.159, C:D.159, C:K.215, C:G.304, C:K.338 pi-Stacking: C:Y.308 ADP.7: 15 residues within 4Å: Chain D: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.13, D:S.16, D:D.159, D:D.159, D:D.159, D:K.215, D:G.304, D:K.338 pi-Stacking: D:Y.308 ADP.9: 15 residues within 4Å: Chain E: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:D.13, E:S.16, E:D.159, E:D.159, E:D.159, E:K.215, E:G.304, E:K.338 pi-Stacking: E:Y.308 ADP.11: 15 residues within 4Å: Chain F: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:D.13, F:S.16, F:D.159, F:D.159, F:D.159, F:K.215, F:G.304, F:K.338 pi-Stacking: F:Y.308 ADP.13: 15 residues within 4Å: Chain G: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.14 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:D.13, G:S.16, G:D.159, G:D.159, G:D.159, G:K.215, G:G.304, G:K.338 pi-Stacking: G:Y.308 ADP.15: 15 residues within 4Å: Chain H: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.16 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:D.13, H:S.16, H:D.159, H:D.159, H:D.159, H:K.215, H:G.304, H:K.338 pi-Stacking: H:Y.308 ADP.17: 15 residues within 4Å: Chain I: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:D.13, I:S.16, I:D.159, I:D.159, I:D.159, I:K.215, I:G.304, I:K.338 pi-Stacking: I:Y.308 ADP.19: 15 residues within 4Å: Chain J: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.20 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:D.13, J:S.16, J:D.159, J:D.159, J:D.159, J:K.215, J:G.304, J:K.338 pi-Stacking: J:Y.308 ADP.21: 15 residues within 4Å: Chain K: D.13, G.15, S.16, L.18, G.158, D.159, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:D.13, K:S.16, K:D.159, K:D.159, K:D.159, K:K.215, K:G.304, K:K.338 pi-Stacking: K:Y.308

11 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.139, D.156 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.139, D.156 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.139, D.156 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.139, D.156 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.139, D.156 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: Q.139, D.156 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: Q.139, D.156 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: Q.139, D.156 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain I: Q.139, D.156 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: Q.139, D.156 Ligands: ADP.19 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain K: Q.139, D.156 Ligands: ADP.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwebach, C.L. et al., Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling. Bone Res (2020)

Release Date

2020-12-09

Peptides

Actin, alpha skeletal muscle: ABCDEFGHIJK
LCP1: LMNOPQRSTUV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
a

M
b

N
c

O
d

P
e

Q
f

R
g

S
h

T
i

U
j

V
k

Actin, alpha skeletal muscle

LCP1

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