SMTL ID : 8cdq.1

Plasmodium falciparum Myosin A full-length, post-rigor state complexed to the inhibitor KNX-002 and Mg.ATP-gamma-S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: V.501, F.502, E.505, L.519, K.520, L.698 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.505, A:K.520, A:K.520 Water bridges: A:E.505 GOL.2: 7 residues within 4Å: Chain A: E.406, I.409, W.423, R.606, G.607, D.608, L.609 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.409, A:R.606, A:D.608, A:L.609 GOL.3: 6 residues within 4Å: Chain A: F.270, L.271, L.272, E.441, L.445, Q.648 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.271, A:L.272, A:E.441, A:Q.648 GOL.5: 5 residues within 4Å: Chain A: T.129, P.132, I.134, T.169, E.173 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.662

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: N.148, R.152 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.148 Water bridges: A:N.148, A:E.149 Salt bridges: A:R.152 SO4.12: 5 residues within 4Å: Chain B: T.160, S.162 Chain C: S.20, D.21, H.22 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.160, B:S.162, C:D.21, C:H.22 Salt bridges: C:H.22

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 7 residues within 4Å: Chain A: N.496, D.499, I.500, E.503, I.656, N.657, T.659 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.496, A:E.503, A:I.656 EDO.8: 4 residues within 4Å: Chain A: E.7, E.192, K.682, I.685 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.7 Water bridges: A:E.192

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 9 residues within 4Å: Chain A: E.273, F.471, E.474, F.476, N.478, E.482, Q.483, I.486 Ligands: KQ0.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.474, A:E.474, A:Q.483 Water bridges: A:K.600

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.9: 19 residues within 4Å: Chain A: N.138, P.139, Y.140, K.141, E.192, S.193, G.194, A.195, G.196, K.197, T.198, E.199, Q.203, N.242, N.244, S.245, S.246, F.471 Ligands: MG.10 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:N.138, A:K.141, A:G.194, A:A.195, A:G.196, A:K.197, A:K.197, A:T.198, A:E.199, A:Q.203, A:N.242, A:N.244, A:S.246, A:S.246 Water bridges: A:Y.127, A:N.145, A:E.199, A:Q.203, A:N.244, A:S.246, A:S.246, A:S.246 Salt bridges: A:K.197

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: T.198, S.246, D.469 Ligands: AGS.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.198, A:S.246, H2O.1, H2O.1

1 x KQ0: 1-(4-methoxyphenyl)-~{N}-[(3-thiophen-2-yl-1~{H}-pyrazol-4-yl)methyl]cyclopropan-1-amine(Non-covalent)

KQ0.11: 13 residues within 4Å: Chain A: S.246, R.247, F.248, G.249, L.271, E.273, I.470, F.471, E.482, F.485, I.486, T.489 Ligands: PG4.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.271, A:E.273, A:I.470, A:F.471, A:F.471, A:E.482, A:E.482, A:I.486, A:T.489 Hydrogen bonds: A:S.246, A:L.271, A:F.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moussaoui, D. et al., Mechanism of small molecule inhibition of Plasmodium falciparum myosin A informs antimalarial drug design. Nat Commun (2023)

Release Date

2023-06-21

Peptides

Myosin-A: A
Myosin A tail domain interacting protein: B
Myosin essential light chain ELC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Myosin-A

Myosin A tail domain interacting protein

Myosin essential light chain ELC

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