Structure of PDB 9fmd Chain 7 Binding Site BS01

Receptor Information

>9fmd Chain 7 (length=390) Species: 9606 (Homo sapiens)

DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQ
IIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQ
IQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMI
RRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATL
PHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDL
YDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMK
EFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY
GRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 9fmd Chain 7 Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9fmd Mechanism for the initiation of spliceosome disassembly.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): G85 T86 G87 K88 T89
• Binding residue (residue number reindexed from 1): G64 T65 G66 K67 T68
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0003729 mRNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008143 poly(A) binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0035368 selenocysteine insertion sequence binding
• GO:0035613 RNA stem-loop binding
• GO:0043021 ribonucleoprotein complex binding

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006364 rRNA processing
• GO:0006397 mRNA processing
• GO:0006406 mRNA export from nucleus
• GO:0006417 regulation of translation
• GO:0008306 associative learning
• GO:0008380 RNA splicing
• GO:0010629 negative regulation of gene expression
• GO:0014070 response to organic cyclic compound
• GO:0017148 negative regulation of translation
• GO:0035640 exploration behavior
• GO:0045727 positive regulation of translation
• GO:0048701 embryonic cranial skeleton morphogenesis
• GO:0051028 mRNA transport
• GO:0072715 cellular response to selenite ion
• GO:0090394 negative regulation of excitatory postsynaptic potential
• GO:0099578 regulation of translation at postsynapse, modulating synaptic transmission
• GO:1904570 negative regulation of selenocysteine incorporation
• GO:1990416 cellular response to brain-derived neurotrophic factor stimulus
• GO:2000622 regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0016607 nuclear speck
• GO:0030425 dendrite
• GO:0035145 exon-exon junction complex
• GO:0043025 neuronal cell body
• GO:0071006 U2-type catalytic step 1 spliceosome
• GO:0071013 catalytic step 2 spliceosome
• GO:0098794 postsynapse
• GO:0098978 glutamatergic synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:9fmd, PDBe:9fmd, PDBj:9fmd
• PDBsum: 9fmd
• PubMed: 38925148
• UniProt: P38919|IF4A3_HUMAN Eukaryotic initiation factor 4A-III (Gene Name=EIF4A3)