SMTL ID : 6i4e.1

Crystal Structure of Plasmodium falciparum actin I in the Mg-ADP state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 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.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: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:N.19, A:N.19, A:D.160, A:G.185, A:K.216, A:E.217, A:E.217, A:G.305, A:K.339 Water bridges: A:K.21, A:K.21, A:K.21, A:K.21, A:K.21, A:G.185, A:T.189 Salt bridges: A:K.21, A:K.21 pi-Stacking: A:Y.309

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

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

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.321, T.322, A.324, S.326 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.321, A:T.322, A:A.324, H2O.8, H2O.11 CA.9: 4 residues within 4Å: Chain A: E.170 Chain B: D.87, G.92, A.94 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:E.170, B:D.87, B:G.92, B:A.94 CA.10: 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.16, H2O.16

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

SCN.4: 3 residues within 4Å: Chain A: S.237, D.238, E.240 No protein-ligand interaction detected (PLIP) SCN.5: 6 residues within 4Å: Chain A: V.8, P.105, P.133, A.134, W.359, T.361 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.359

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

BME.6: 7 residues within 4Å: Chain A: G.23, V.24, R.31, E.96, L.97, R.98 Ligands: BTB.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.97 BME.7: 12 residues within 4Å: Chain A: S.144, L.145, S.147, S.148, V.301, L.302, S.303, P.335, E.337, R.338, S.341 Chain B: Q.73 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.73, A:S.341

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

BTB.8: 8 residues within 4Å: Chain A: R.31, S.32, V.33, N.95, E.96, L.97, R.98 Ligands: BME.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:E.96, A:E.96, A:R.98, A:R.98 Water bridges: A:S.32

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

PEG.11: 8 residues within 4Å: Chain B: A.13, G.14, K.15, L.59, Y.61, Y.89, L.90, N.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.91

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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