Structure of PDB 8t0r Chain f Binding Site BS02

Receptor Information
>8t0r Chain f (length=693) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGASSVLENFVGRDFLP
RGSGIVTRRPLVLQLVNATTEYAEFLHCKGKKFTDFEEVRLEIEAETDRV
TGTNKGISPVPINLRVYSPHVLNLTLVDLPGMTKVPVGDQPPDIEFQIRD
MLMQFVTKENCLILAVSPANSDLANSDALKVAKEVDPQGQRTIGVITKLD
LMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAAERKF
FLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQLLSIE
KEVEEYKNFRPDDPARKTKALLQMVQQFAVDFEKRIEGSGDQIDTYELSG
GARINRIFHERFPFELVKMEFDEKELRREISYAIKNIHGIRTGLFTPDMA
FETIVKKQVKKIREPCLKCVDMVISELISTVRQCTKKLQQYPRLREEMER
IVTTHIREREGRTKEQVMLLIDIELAYMNTNHEDFIGIRKGWLTINNIGI
MKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSK
HIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPEMDPQL
ERQVETIRNLVDSYMAIVNKTVRDLMPKTIMHLMINNTKEFIFSELLANL
YSCGDQNTLMEESAEQAQRRDEMLRMYHALKEALSIIGNINTT
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain8t0r Chain f Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8t0r Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission
Resolution3.97 Å
Binding residue
(original residue number in PDB)		S45 T65
Binding residue
(residue number reindexed from 1)		S37 T57
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.5.5: dynamin GTPase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding
GO:0008017 microtubule binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0019901 protein kinase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0007032 endosome organization
GO:0016185 synaptic vesicle budding from presynaptic endocytic zone membrane
GO:0031623 receptor internalization
GO:0048488 synaptic vesicle endocytosis
GO:0050804 modulation of chemical synaptic transmission
GO:0051260 protein homooligomerization
GO:0051289 protein homotetramerization
GO:0097494 regulation of vesicle size
GO:0099049 clathrin coat assembly involved in endocytosis
GO:0099050 vesicle scission
Cellular Component
GO:0001917 photoreceptor inner segment
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0030117 membrane coat
GO:0030139 endocytic vesicle
GO:0031410 cytoplasmic vesicle
GO:0042583 chromaffin granule
GO:0042995 cell projection
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:0098684 photoreceptor ribbon synapse
GO:0098793 presynapse
GO:0098835 presynaptic endocytic zone membrane
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8t0r, PDBe:8t0r, PDBj:8t0r
PDBsum8t0r
PubMed38663399
UniProtQ05193|DYN1_HUMAN Dynamin-1 (Gene Name=DNM1)

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