SMTL ID : 6w7v.1

Structure of rabbit actin in complex with truncated analog of Mycalolide B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-functional Binders)

CA.1: 3 residues within 4Å: Chain A: G.15, K.20 Ligands: ATP.2 No protein-ligand interaction detected (PLIP)

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

ATP.2: 23 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.76, G.158, D.159, G.160, V.161, G.184, R.185, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: CA.1, LAB.3 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:S.16, A:S.16, A:G.17, A:L.18, A:G.158, A:D.159, A:D.159, A:D.159, A:G.160, A:V.161, A:V.161, A:K.215, A:E.216, A:E.216, A:G.304, A:T.305, A:K.338 Water bridges: A:K.20, A:K.20, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308

1 x LAB: LATRUNCULIN B(Non-covalent)

LAB.3: 20 residues within 4Å: Chain A: G.17, L.18, P.34, S.35, I.36, Q.61, R.64, L.69, Y.71, D.159, G.184, R.185, T.188, T.205, R.208, E.209, R.212, K.215, E.216 Ligands: ATP.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.18, A:P.34, A:I.36, A:I.36, A:Q.61, A:L.69, A:Y.71, A:E.209 Hydrogen bonds: A:Y.71, A:D.159, A:R.185, A:T.188, A:R.212, A:K.215 Salt bridges: A:R.212

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

EDO.4: 5 residues within 4Å: Chain A: K.293, D.294, A.297, N.298, K.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.294, A:D.294 Water bridges: A:A.297, A:K.328 EDO.6: 6 residues within 4Å: Chain A: Y.200, S.201, F.202, E.207, L.244, D.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.201, A:E.207 EDO.7: 4 residues within 4Å: Chain A: Y.168, L.173, D.288, I.291 No protein-ligand interaction detected (PLIP)

1 x TFJ: (1E,3R,4R,5S,6R,9S,10S,12S)-12-[(4-aminobutanoyl)oxy]-1-[ethyl(formyl)amino]-4,10-dimethoxy-3,5,9,13-tetramethyltetradec-1-en-6-yl (2R)-oxolane-2-carboxylate(Non-covalent)

TFJ.5: 19 residues within 4Å: Chain A: Y.135, A.137, I.138, V.141, Y.145, A.146, S.147, G.148, R.149, T.150, G.170, Y.171, A.172, I.347, L.348, L.351, T.353, F.354, M.357 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.145, A:Y.145, A:I.347, A:I.347, A:L.348, A:L.351 Hydrogen bonds: A:A.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pipaliya, B.V. et al., Truncated Actin-Targeting Macrolide Derivative Blocks Cancer Cell Motility and Invasion of Extracellular Matrix. J.Am.Chem.Soc. (2021)

Release Date

2020-10-21

Peptides

Actin, alpha skeletal muscle: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Actin, alpha skeletal muscle

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