SMTL ID : 3m6g.1 (2 other biounits)

Crystal structure of actin in complex with lobophorolide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

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

ATP.2: 20 residues within 4Å: Chain A: G.13, S.14, G.15, L.16, K.18, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:S.14, A:S.14, A:G.15, A:L.16, A:G.156, A:D.157, A:D.157, A:D.157, A:G.158, A:V.159, A:V.159, A:K.213, A:E.214, A:G.302, A:K.336 Water bridges: A:K.18, A:K.18, A:D.154, A:D.154, A:D.154, A:D.154, A:D.157, A:G.182, A:R.210, A:E.214, A:Y.306, A:K.336 Salt bridges: A:K.18, A:K.18 pi-Stacking: A:Y.306 ATP.7: 22 residues within 4Å: Chain B: G.13, S.14, G.15, L.16, K.18, G.74, G.156, D.157, G.158, V.159, G.182, R.183, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.6 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:S.14, B:S.14, B:G.15, B:L.16, B:D.157, B:D.157, B:G.158, B:V.159, B:V.159, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303 Water bridges: B:K.18, B:K.18, B:Q.137, B:D.154, B:D.154, B:G.156, B:D.157, B:G.182, B:R.210, B:Y.306, B:K.336, B:K.336 Salt bridges: B:K.18, B:K.18 pi-Stacking: B:Y.306

2 x LO3: (1S,3S,4S,5S,7R,8S,9R,12E,14E,16R,17R,19R)-16-hydroxy-9-{(1S,2S,3S)-2-hydroxy-5-[(2S,4R,6S)-4-methoxy-6-methyltetrahydro-2H-pyran-2-yl]-1,3-dimethylpentyl}-3,5,7,17-tetramethoxy-8,14-dimethyl-11H-spiro[10,23-dioxabicyclo[17.3.1]tricosa-12,14,20-triene-4,2'-oxiran]-11-one(Non-covalent)

LO3.3: 19 residues within 4Å: Chain A: Y.133, Y.143, A.144, S.145, G.146, R.147, I.345, L.346, L.349, T.351, M.355 Chain B: G.23, D.24, D.25, I.341, S.344, I.345, S.348 Ligands: LO3.8 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.341, B:I.345, A:Y.143, A:Y.143, A:Y.143 Hydrogen bonds: A:Y.143, A:A.144 LO3.8: 20 residues within 4Å: Chain A: G.23, D.24, D.25, I.341, S.344, I.345, S.348, L.349 Chain B: Y.133, Y.143, A.144, S.145, G.146, R.147, I.345, L.346, L.349, T.351, M.355 Ligands: LO3.3 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.341, A:I.345, B:Y.143, B:Y.143, B:Y.143, B:I.345, B:I.345, B:L.346 Hydrogen bonds: B:A.144

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: E.205 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.205, H2O.3, H2O.4, H2O.7, H2O.8 CA.5: 1 residues within 4Å: Chain A: V.30 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:V.30, H2O.5, H2O.6, H2O.10, H2O.10 CA.9: 3 residues within 4Å: Chain B: Q.354, W.356, E.361 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.354, B:W.356, B:E.361, H2O.24, H2O.26 CA.10: 1 residues within 4Å: Chain B: V.30 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:V.30, H2O.15, H2O.20, H2O.24, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blain, J.C. et al., Two molecules of lobophorolide cooperate to stabilize an actin dimer using both their "ring" and "tail" region. Chem.Biol. (2010)

Release Date

2010-09-08

Peptides

Actin, alpha skeletal muscle: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Actin, alpha skeletal muscle

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