SMTL ID : 9l2n.1

Crystal structure of Cytochalasin D bound to a filamentous conformation actin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.156, D.157, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: PO4.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:S.14, A:G.15, A:L.16, A:D.157, A:D.157, A:G.158, A:K.213, A:G.302, A:K.336 Water bridges: A:K.18, A:K.18, A:K.18, A:E.214, A:E.214, A:E.214, A:E.214, A:E.214, A:M.305 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: S.14, G.74, Q.137, G.156, D.157, G.158, V.159 Ligands: ADP.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.14, A:G.156, A:G.158, A:V.159 Water bridges: A:Q.137, A:Q.137, A:Q.137, A:D.154, A:D.154, A:D.154, A:V.159 PO4.4: 1 residues within 4Å: Chain A: R.95 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.91, A:R.95, A:R.95 Salt bridges: A:R.95 PO4.5: 2 residues within 4Å: Chain A: R.39, H.40 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.39, A:R.39, A:R.39 Salt bridges: A:R.39, A:H.40

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

MG.3: 2 residues within 4Å: Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP)

1 x CY9: (3S,3aR,4S,6S,6aR,7E,10S,12R,13E,15R,15aR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1,11-dioxo-2,3,3a,4,5,6,6a,9,10,11,12,15-dodecahydro-1H-cycloundeca[d]isoindol-15-yl acetate(Non-covalent)

CY9.6: 15 residues within 4Å: Chain A: Y.133, A.135, I.136, V.139, Y.143, G.168, Y.169, A.170, P.172, F.352, M.355, C.374, F.375 Chain B: Y.111, V.114 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.136, A:V.139, A:Y.169, A:Y.169, A:F.352, A:F.375, A:F.375, B:Y.111, B:V.114 Hydrogen bonds: A:I.136, A:Y.143, A:G.168, A:Y.169, A:A.170 Water bridges: A:Y.133, A:Y.169, A:A.170

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: E.167 Chain B: D.117, G.122, P.124 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.117, B:P.124, A:E.167, H2O.14, H2O.27 CA.8: 4 residues within 4Å: Chain B: G.71, D.72, E.105, V.154 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:E.105, B:V.154, H2O.26, H2O.26

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

EDO.9: 6 residues within 4Å: Chain B: E.48, I.49, W.50, P.59, V.60, H.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.48, B:E.48, B:I.49, B:H.65 Water bridges: B:K.62 EDO.10: 3 residues within 4Å: Chain B: Y.80, D.92, R.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.92, B:R.137 Water bridges: B:Y.80, B:Y.80, B:Y.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitani, T. et al., Microscopic and structural observations of actin filament capping and severing by cytochalasin D. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-02

Peptides

Actin, alpha skeletal muscle: A
Actin-binding protein fragmin P: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Actin, alpha skeletal muscle

Actin-binding protein fragmin P

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