SMTL ID : 6i4m.1

Crystal Structure of Plasmodium berghei actin II in the Mg-ADP state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: G.15, S.16, G.17, M.18, K.20, G.158, D.159, G.160, V.161, G.184, R.185, R.212, K.215, E.216, G.304, G.305, T.306, M.308, Y.309, K.339 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.15, A:S.16, A:S.16, A:G.17, A:M.18, A:D.159, A:G.184, A:K.215, A:E.216, A:E.216, A:E.216, A:G.305, A:T.306, A:K.339 Water bridges: A:K.20, A:K.20, A:K.20, A:K.20, A:K.339 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.309

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

MG.2: 4 residues within 4Å: Chain A: G.15, K.20, V.342 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 8 residues within 4Å: Chain A: A.146, S.147, P.335, E.337, R.338, S.341, I.344 Chain B: Q.73 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.73 Water bridges: A:S.147 SCN.4: 7 residues within 4Å: Chain A: Y.282, M.286, I.290, R.293, Y.297, P.325, M.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.297

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.169 Chain B: D.87, G.92, A.94 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.87, B:G.92, B:A.94, A:E.169, H2O.16 CA.6: 6 residues within 4Å: Chain B: G.43, D.44, C.71, S.72, E.75, V.123 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.44, B:E.75, B:V.123, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumpula, E.P. et al., Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation. Plos Biol. (2019)

Release Date

2019-06-26

Peptides

Actin-2: A
Gelsolin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Actin-2

Gelsolin

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