Structure of PDB 3m6g Chain A Binding Site BS02

Receptor Information

>3m6g Chain A (length=353) Species: 9986 (Oryctolagus cuniculus)

TALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPSYVGDEAQSKRGILTLK
YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEG
YALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCY
VALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIG
MESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEIT
ALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPS
IVH

Ligand information

• Ligand ID: LO3
• InChI: InChI=1S/C42H70O12/c1-25-14-17-39(44)54-41(29(5)40(45)26(2)15-16-32-20-33(46-6)19-27(3)52-32)28(4)35(47-7)23-38(50-10)42(24-51-42)37(49-9)22-31-13-11-12-30(53-31)21-36(48-8)34(43)18-25/h11-12,14,17-18,26-38,40-41,43,45H,13,15-16,19-24H2,1-10H3/b17-14+,25-18+/t26-,27-,28-,29-,30-,31-,32-,33+,34+,35+,36+,37-,38-,40-,41-,42-/m0/s1
• InChIKey: YPLVKLZVFQFTLN-NNZJXHHNSA-N
• SMILES:
  CACTVS 3.370: CO[C@@H]1C[C@H](C)O[C@@H](CC[C@H](C)[C@H](O)[C@H](C)[C@H]2OC(=O)\C=C\C(=C\[C@@H](O)[C@@H](C[C@H]3O[C@@H](CC=C3)C[C@H](OC)[C@@]4(CO4)[C@H](C[C@@H](OC)[C@@H]2C)OC)OC)C)C1
  OpenEye OEToolkits 1.7.0: C[C@H]1C[C@H](C[C@@H](O1)CC[C@H](C)[C@@H]([C@H](C)[C@@H]2[C@H]([C@@H](C[C@@H]([C@]3(CO3)[C@H](C[C@@H]4CC=C[C@H](O4)C[C@H]([C@@H](/C=C(/C=C/C(=O)O2)\C)O)OC)OC)OC)OC)C)O)OC
  CACTVS 3.370: CO[CH]1C[CH](C)O[CH](CC[CH](C)[CH](O)[CH](C)[CH]2OC(=O)C=CC(=C[CH](O)[CH](C[CH]3O[CH](CC=C3)C[CH](OC)[C]4(CO4)[CH](C[CH](OC)[CH]2C)OC)OC)C)C1
  OpenEye OEToolkits 1.7.0: CC1CC(CC(O1)CCC(C)C(C(C)C2C(C(CC(C3(CO3)C(CC4CC=CC(O4)CC(C(C=C(C=CC(=O)O2)C)O)OC)OC)OC)OC)C)O)OC
  ACDLabs 12.01: O=C3OC(C(C)C(OC)CC(OC)C1(OC1)C(OC)CC2OC(C=CC2)CC(OC)C(O)C=C(C=C3)C)C(C)C(O)C(CCC4OC(CC(OC)C4)C)C
• Formula: C42 H70 O12
• Name: (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
• ZINC: ZINC000098209124
• PDB chain: 3m6g Chain A Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3m6g Two molecules of lobophorolide cooperate to stabilize an actin dimer using both their "ring" and "tail" region.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y143 A144 S145 G146 R147 L346 L349 M355
• Binding residue (residue number reindexed from 1): Y125 A126 S127 G128 R129 L328 L331 M337
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003785 actin monomer binding
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005523 tropomyosin binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0019904 protein domain specific binding
• GO:0031013 troponin I binding
• GO:0031432 titin binding
• GO:0032036 myosin heavy chain binding
• GO:0042802 identical protein binding
• GO:0048306 calcium-dependent protein binding
• GO:0140660 cytoskeletal motor activator activity

Biological Process

• GO:0010628 positive regulation of gene expression
• GO:0030041 actin filament polymerization
• GO:0030240 skeletal muscle thin filament assembly
• GO:0048741 skeletal muscle fiber development
• GO:0051017 actin filament bundle assembly
• GO:0090131 mesenchyme migration

Cellular Component

• GO:0001725 stress fiber
• GO:0005737 cytoplasm
• GO:0005856 cytoskeleton
• GO:0005865 striated muscle thin filament
• GO:0005884 actin filament
• GO:0030027 lamellipodium
• GO:0030175 filopodium
• GO:0031941 filamentous actin
• GO:0032432 actin filament bundle
• GO:0044297 cell body
• GO:0098723 skeletal muscle myofibril

External links

• PDB: RCSB:3m6g, PDBe:3m6g, PDBj:3m6g
• PDBsum: 3m6g
• PubMed: 20797609
• UniProt: P68135|ACTS_RABIT Actin, alpha skeletal muscle (Gene Name=ACTA1)