SMTL ID : 7whg.1

Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-2-1-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: 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: CA.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.16, A:G.17, A:L.18, A:L.18, A:D.159, A:D.159, A:D.159, A:K.215, A:E.216, A:G.304, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.4: 17 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.184, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: CA.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, 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

9 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.13, Q.139, D.156 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: V.32, D.58 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.58 CA.5: 3 residues within 4Å: Chain B: D.13, Q.139 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) CA.6: 5 residues within 4Å: Chain C: G.22, D.23, E.45, Y.95, A.96 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:G.22, C:D.23, C:E.45, C:E.45, C:A.96 CA.7: 4 residues within 4Å: Chain B: D.27 Chain C: D.102, V.103, L.220 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.102, C:V.103, C:L.220, B:D.27 CA.8: 4 residues within 4Å: Chain C: E.124, E.147, D.148, E.170 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.124, C:E.147, C:D.148, C:E.170 CA.9: 4 residues within 4Å: Chain C: D.182, R.185, G.187, Q.189 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.182, C:D.182, C:R.185, C:G.187 CA.10: 5 residues within 4Å: Chain B: E.169 Chain C: D.57, G.62, A.63, A.64 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:G.62, C:A.64, B:E.169 CA.11: 4 residues within 4Å: Chain C: R.120, E.124, E.147, D.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.124, C:E.124, C:D.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akil, C. et al., Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis. Commun Biol (2022)

Release Date

2022-09-21

Peptides

Actin, alpha skeletal muscle: AB
Lokiarchaeota gelsolin (2DGel): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

Actin, alpha skeletal muscle

Lokiarchaeota gelsolin (2DGel)

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