SMTL ID : 7ad9.1

Structure of the Lifeact-F-actin complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

Ligands

5 x HYP- ALA- TRP- EEP- ALA- DTH- CYS: Phalloidin(Non-covalent)

HYP-ALA-TRP-EEP-ALA-DTH-CYS.1: 7 residues within 4Å: Chain B: E.74, I.77, L.112, P.114, R.179, D.181 Chain D: R.292 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.74, B:I.77, B:P.114 HYP-ALA-TRP-EEP-ALA-DTH-CYS.2: 14 residues within 4Å: Chain B: T.196, R.198, G.199, Y.200, S.201, E.207, L.244 Chain D: E.74, I.77, L.112, P.114, R.179, D.181 Chain F: R.292 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:E.74, D:I.77, D:P.114, B:T.196, B:Y.200, B:L.244 Hydrogen bonds: B:G.199, B:S.201, B:S.201, B:S.201 HYP-ALA-TRP-EEP-ALA-DTH-CYS.3: 13 residues within 4Å: Chain D: T.196, G.199, Y.200, S.201, E.207, L.244 Chain F: E.74, I.77, L.112, P.114, R.179, D.181 Chain H: R.292 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:T.196, D:Y.200, D:L.244, F:E.74, F:I.77, F:P.114 Hydrogen bonds: D:S.201, D:S.201, D:S.201 HYP-ALA-TRP-EEP-ALA-DTH-CYS.4: 13 residues within 4Å: Chain F: T.196, G.199, Y.200, S.201, E.207, L.244 Chain H: E.74, I.77, L.112, P.114, R.179, D.181 Chain J: R.292 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain H Hydrophobic interactions: F:T.196, F:Y.200, F:L.244, H:E.74, H:I.77, H:P.114 Hydrogen bonds: F:G.199, F:S.201, F:S.201, F:S.201 HYP-ALA-TRP-EEP-ALA-DTH-CYS.5: 12 residues within 4Å: Chain H: T.196, G.199, Y.200, S.201, E.207, L.244 Chain J: E.74, I.77, L.112, P.114, R.179, D.181 9 PLIP interactions: 6 interactions with chain H, 3 interactions with chain J Hydrophobic interactions: H:T.196, H:Y.200, H:L.244, J:E.74, J:I.77, J:P.114 Hydrogen bonds: H:S.201, H:S.201, H:S.201

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

ADP.6: 19 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.7, PO4.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.17, B:L.18, B:D.159, B:D.159, B:D.159, B:K.215, B:G.304, B:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.9: 19 residues within 4Å: Chain D: 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.10, PO4.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.17, D:L.18, D:D.159, D:D.159, D:D.159, D:K.215, D:G.304, D:K.338 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.12: 19 residues within 4Å: Chain F: 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.13, PO4.14 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.17, F:L.18, F:D.159, F:D.159, F:D.159, F:K.215, F:G.304, F:K.338 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.15: 19 residues within 4Å: Chain H: 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.16, PO4.17 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.17, H:L.18, H:D.159, H:D.159, H:D.159, H:K.215, H:G.304, H:K.338 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308 ADP.18: 19 residues within 4Å: Chain J: 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.19, PO4.20 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.17, J:L.18, J:D.159, J:D.159, J:D.159, J:K.215, J:G.304, J:K.338 Salt bridges: J:K.20, J:K.20 pi-Stacking: J:Y.308

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

MG.7: 2 residues within 4Å: Ligands: ADP.6, PO4.8 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Ligands: ADP.9, PO4.11 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Ligands: ADP.12, PO4.14 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Ligands: ADP.15, PO4.17 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Ligands: ADP.18, PO4.20 No protein-ligand interaction detected (PLIP)

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

PO4.8: 7 residues within 4Å: Chain B: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.6, MG.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.16, B:Q.139, B:G.160, B:V.161 PO4.11: 7 residues within 4Å: Chain D: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.9, MG.10 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.16, D:Q.139, D:G.160, D:V.161 PO4.14: 7 residues within 4Å: Chain F: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.12, MG.13 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.16, F:Q.139, F:G.160, F:V.161 PO4.17: 7 residues within 4Å: Chain H: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.15, MG.16 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:S.16, H:Q.139, H:G.160, H:V.161 PO4.20: 7 residues within 4Å: Chain J: G.15, S.16, Q.139, G.160, V.161 Ligands: ADP.18, MG.19 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:S.16, J:Q.139, J:G.160, J:V.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Belyy, A. et al., Structure of the Lifeact-F-actin complex. Plos Biol. (2020)

Release Date

2020-10-28

Peptides

Lifeact: ACEGI
Actin, alpha skeletal muscle: BDFHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
L

G
E

I
G

B
B

D
D

F
H

H
F

J
I

Lifeact

Actin, alpha skeletal muscle

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