SMTL ID : 6i4k.1

Crystal Structure of Plasmodium falciparum actin I (G115A mutant) in the Ca-ATP state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 23 residues within 4Å: Chain A: G.16, S.17, G.18, N.19, K.21, G.77, G.159, D.160, G.161, V.162, G.185, R.186, T.189, R.213, K.216, E.217, G.304, G.305, T.306, M.308, Y.309, K.339 Ligands: CA.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:N.19, A:N.19, A:N.19, A:G.77, A:G.159, A:D.160, A:G.161, A:V.162, A:K.216, A:E.217, A:E.217, A:G.305, A:T.306, A:T.306, A:K.339 Water bridges: A:K.21, A:K.21, A:T.189, A:R.213, A:K.339 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:Y.309

3 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: G.16, K.21 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) CA.7: 6 residues within 4Å: Chain B: G.43, D.44, C.71, E.75, G.122, 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.17, H2O.18 CA.8: 5 residues within 4Å: Chain A: E.170 Chain B: D.87, G.92, A.94, Q.96 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.87, B:A.94, A:E.170, H2O.18, H2O.18

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

SCN.3: 5 residues within 4Å: Chain A: G.23, V.24, R.31, L.97 Ligands: BTB.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.31 SCN.9: 7 residues within 4Å: Chain B: R.23, V.32, P.33, L.36, F.41, Y.46, K.119 No protein-ligand interaction detected (PLIP)

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 7 residues within 4Å: Chain A: R.31, S.32, N.95, E.96, L.97, R.98 Ligands: SCN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.32, A:S.32, A:R.98, A:R.98 Water bridges: A:R.31, A:N.95

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: A.55, F.56, V.57, E.60, K.87, H.90, H.91, N.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.57, A:E.60, A:H.90, A:H.91, A:N.95

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: T.321, T.322, A.324, S.326 Ligand excluded by PLIP

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.10: 7 residues within 4Å: Chain B: A.13, G.14, K.15, L.59, Y.61, Y.89, L.90 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.61

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-1: A
Gelsolin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Actin-1

Gelsolin

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