SMTL ID : 6i4f.1

Crystal Structure of Plasmodium falciparum actin I (A272W mutant) in the Mg-K-ATP/ADP state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.213, K.216, E.217, G.304, G.305, T.306, M.308, Y.309, K.339 Ligands: ADP.2, MG.3, K.4 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:G.159, A:D.160, A:G.161, A:V.162, A:K.216, A:E.217, A:E.217, A:E.217, A:G.305, A:T.306, A:K.339 Water bridges: A:K.21, A:K.21, A:K.21, A:K.21, A:K.21, A:K.21, A:T.189 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:Y.309

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

ADP.2: 22 residues within 4Å: Chain A: G.16, S.17, G.18, N.19, K.21, G.159, D.160, G.161, 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: ATP.1, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.17, A:G.18, A:N.19, A:D.160, A:K.216, A:E.217, A:E.217, A:G.305, A:T.306, A:K.339 Water bridges: A:N.19, A:K.21, A:K.21, A:K.21, A:K.21, A:T.189, A:E.217, A:M.308 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:Y.309

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

MG.3: 4 residues within 4Å: Chain A: G.16, K.21 Ligands: ATP.1, ADP.2 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: D.157, S.158, G.159, V.162, S.163, H.164 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.157, A:V.162, H2O.2, H2O.4

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

BTB.5: 6 residues within 4Å: Chain A: R.31, S.32, N.95, E.96, L.97, R.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.96, A:R.98, A:R.98 Water bridges: A:S.32

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

PEG.6: 9 residues within 4Å: Chain A: S.147, S.148, R.150, K.331, V.333, P.335, P.336 Chain B: Q.73, R.98 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.150, A:R.150, A:K.331 Water bridges: A:S.147, B:R.98, B:R.98

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: K.294, Y.297, G.298, K.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.329, A:K.329

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

CL.8: 4 residues within 4Å: Chain A: T.321, T.322, A.324, S.326 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.18, H2O.19 CA.10: 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.17, H2O.18

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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