SMTL ID : 6tu4.1

Structure of Plasmodium Actin1 filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ADP.15 No protein-ligand interaction detected (PLIP)

5 x 9UE: Jasplakinolide(Non-covalent)

9UE.2: 13 residues within 4Å: Chain A: H.197, R.199, G.200, Y.201, G.202, E.208, L.245, I.250 Chain D: H.76, I.78, P.115, R.180, D.182 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.201, A:L.245, D:I.78 Hydrogen bonds: A:G.200, A:G.202, A:G.202 9UE.5: 14 residues within 4Å: Chain A: H.76, I.78, L.113, P.115, R.180, D.182 Chain B: H.197, R.199, G.200, Y.201, G.202, E.208, L.245, I.250 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.201, B:L.245, A:I.78 Hydrogen bonds: B:G.200, B:G.202, B:G.202, A:R.180 9UE.8: 13 residues within 4Å: Chain B: H.76, I.78, L.113, P.115, D.182 Chain C: H.197, R.199, G.200, Y.201, G.202, E.208, L.245, I.250 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.197, C:Y.201, C:L.245, B:I.78 Hydrogen bonds: C:G.200, C:G.202, C:G.202 pi-Stacking: C:H.197 9UE.11: 14 residues within 4Å: Chain D: H.197, R.199, G.200, Y.201, G.202, E.208, L.245, I.250 Chain E: H.76, I.78, L.113, P.115, R.180, D.182 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.201, D:L.245, E:I.78 Hydrogen bonds: D:G.200, D:G.202, D:G.202 9UE.14: 8 residues within 4Å: Chain E: H.197, R.199, G.200, Y.201, G.202, E.208, L.245, I.250 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.201, E:Y.201, E:L.245 Hydrogen bonds: E:G.200, E:G.202, E:G.202

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

ADP.3: 15 residues within 4Å: Chain A: G.16, S.17, G.18, N.19, K.21, G.159, D.160, R.213, K.216, E.217, G.305, T.306, Y.309, K.339 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.17, A:G.18, A:N.19, A:N.19, A:D.160, A:D.160, A:K.216, A:E.217, A:G.305, A:T.306, A:K.339 Water bridges: A:D.14, A:S.17, A:K.21, A:K.21, A:D.160, A:V.162, A:G.185 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:Y.309 ADP.6: 16 residues within 4Å: Chain B: G.16, S.17, G.18, N.19, K.21, G.159, D.160, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.4 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:S.17, B:G.18, B:N.19, B:N.19, B:D.160, B:D.160, B:K.216, B:E.217, B:G.305, B:T.306, B:K.339 Water bridges: B:D.14, B:S.17, B:K.21, B:K.21, B:D.160, B:V.162, B:G.185 Salt bridges: B:K.21, B:K.21 pi-Stacking: B:Y.309 ADP.9: 17 residues within 4Å: Chain C: G.16, S.17, G.18, N.19, K.21, G.159, D.160, R.213, K.216, E.217, G.304, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.7 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:S.17, C:G.18, C:N.19, C:N.19, C:D.160, C:D.160, C:K.216, C:E.217, C:G.305, C:T.306, C:K.339 Water bridges: C:D.14, C:N.15, C:S.17, C:K.21, C:K.21, C:D.160, C:V.162, C:T.189 Salt bridges: C:K.21, C:K.21 pi-Stacking: C:Y.309 ADP.12: 17 residues within 4Å: Chain D: G.16, S.17, G.18, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:S.17, D:G.18, D:N.19, D:N.19, D:D.160, D:D.160, D:D.160, D:K.216, D:E.217, D:G.305, D:K.339 Water bridges: D:D.14, D:S.17, D:K.21, D:K.21, D:S.158, D:V.162 Salt bridges: D:K.21, D:K.21 pi-Stacking: D:Y.309 ADP.15: 17 residues within 4Å: Chain E: G.16, S.17, G.18, N.19, K.21, G.159, D.160, G.185, R.213, K.216, E.217, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.13 21 PLIP interactions: 21 interactions with chain E Hydrogen bonds: E:S.17, E:G.18, E:N.19, E:N.19, E:D.160, E:D.160, E:D.160, E:K.216, E:E.217, E:G.305, E:T.306, E:K.339 Water bridges: E:D.14, E:S.17, E:K.21, E:K.21, E:V.162, E:T.189 Salt bridges: E:K.21, E:K.21 pi-Stacking: E:Y.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vahokoski, J. et al., High-resolution structures of malaria parasite actomyosin and actin filaments. Plos Pathog. (2022)

Release Date

2021-01-13

Peptides

Actin-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

Actin-1

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