SMTL ID : 7q8b.1

Leishmania major actin filament in ADP-Pi state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.12, Q.138 Ligands: ADP.2, PO4.3 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: D.12, Q.138 Ligands: ADP.5, PO4.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: D.12, Q.138 Ligands: ADP.8, PO4.9 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: D.12, Q.138 Ligands: ADP.11, PO4.12 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain E: D.12, Q.138 Ligands: ADP.14, PO4.15 No protein-ligand interaction detected (PLIP)

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.2: 17 residues within 4Å: Chain A: G.14, S.15, G.16, M.17, K.19, G.157, D.158, K.214, E.215, G.302, G.303, S.304, M.306, F.307, K.337 Ligands: MG.1, PO4.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.15, A:G.16, A:M.17, A:D.158, A:D.158, A:E.215, A:G.303, A:K.337 Salt bridges: A:K.19, A:K.19 pi-Stacking: A:F.307 ADP.5: 17 residues within 4Å: Chain B: G.14, S.15, G.16, M.17, K.19, G.157, D.158, K.214, E.215, G.302, G.303, S.304, M.306, F.307, K.337 Ligands: MG.4, PO4.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.15, B:G.16, B:M.17, B:D.158, B:D.158, B:E.215, B:G.303, B:K.337 Salt bridges: B:K.19, B:K.19 pi-Stacking: B:F.307 ADP.8: 17 residues within 4Å: Chain C: G.14, S.15, G.16, M.17, K.19, G.157, D.158, K.214, E.215, G.302, G.303, S.304, M.306, F.307, K.337 Ligands: MG.7, PO4.9 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.15, C:G.16, C:M.17, C:D.158, C:D.158, C:E.215, C:G.303, C:K.337 Salt bridges: C:K.19, C:K.19 pi-Stacking: C:F.307 ADP.11: 17 residues within 4Å: Chain D: G.14, S.15, G.16, M.17, K.19, G.157, D.158, K.214, E.215, G.302, G.303, S.304, M.306, F.307, K.337 Ligands: MG.10, PO4.12 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.15, D:G.16, D:M.17, D:D.158, D:D.158, D:E.215, D:G.303, D:K.337 Salt bridges: D:K.19, D:K.19 pi-Stacking: D:F.307 ADP.14: 17 residues within 4Å: Chain E: G.14, S.15, G.16, M.17, K.19, G.157, D.158, K.214, E.215, G.302, G.303, S.304, M.306, F.307, K.337 Ligands: MG.13, PO4.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.15, E:G.16, E:M.17, E:D.158, E:D.158, E:E.215, E:G.303, E:K.337 Salt bridges: E:K.19, E:K.19 pi-Stacking: E:F.307

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

PO4.3: 9 residues within 4Å: Chain A: S.15, G.75, Q.138, G.157, D.158, G.159, V.160 Ligands: MG.1, ADP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.15, A:Q.138, A:G.157, A:D.158, A:G.159, A:V.160, A:V.160 PO4.6: 9 residues within 4Å: Chain B: S.15, G.75, Q.138, G.157, D.158, G.159, V.160 Ligands: MG.4, ADP.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.15, B:Q.138, B:G.157, B:D.158, B:G.159, B:V.160, B:V.160 PO4.9: 9 residues within 4Å: Chain C: S.15, G.75, Q.138, G.157, D.158, G.159, V.160 Ligands: MG.7, ADP.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.15, C:Q.138, C:G.157, C:D.158, C:G.159, C:V.160, C:V.160 PO4.12: 9 residues within 4Å: Chain D: S.15, G.75, Q.138, G.157, D.158, G.159, V.160 Ligands: MG.10, ADP.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.15, D:Q.138, D:G.157, D:D.158, D:G.159, D:V.160, D:V.160 PO4.15: 9 residues within 4Å: Chain E: S.15, G.75, Q.138, G.157, D.158, G.159, V.160 Ligands: MG.13, ADP.14 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.15, E:Q.138, E:G.157, E:D.158, E:G.159, E:V.160, E:V.160

Links

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Citation

Kotila, T. et al., Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite. Nat Commun (2022)

Release Date

2022-05-18

Peptides

Actin: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Actin

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