Structure of PDB 6iyb Chain C Binding Site BS01

Receptor Information
>6iyb Chain C (length=171) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRL
VTMQIWDTAGLERFQSGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFL
IQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAK
EAINVEQAFQTIARNALKQET
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 chain6iyb Chain C Residue 1301 [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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PDB6iyb Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting.
Resolution2.091 Å
Binding residue
(original residue number in PDB)		T22 T40
Binding residue
(residue number reindexed from 1)		T16 T34
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0031267 small GTPase binding
GO:1905394 retromer complex binding
Biological Process
GO:0000045 autophagosome assembly
GO:0006622 protein targeting to lysosome
GO:0006897 endocytosis
GO:0006914 autophagy
GO:0007174 epidermal growth factor catabolic process
GO:0008333 endosome to lysosome transport
GO:0009617 response to bacterium
GO:0015031 protein transport
GO:0016042 lipid catabolic process
GO:0019076 viral release from host cell
GO:0022615 protein to membrane docking
GO:0036466 synaptic vesicle recycling via endosome
GO:0042147 retrograde transport, endosome to Golgi
GO:0045022 early endosome to late endosome transport
GO:0045453 bone resorption
GO:0045732 positive regulation of protein catabolic process
GO:0046907 intracellular transport
GO:0048524 positive regulation of viral process
GO:0051650 establishment of vesicle localization
GO:0061724 lipophagy
GO:0090382 phagosome maturation
GO:0090383 phagosome acidification
GO:0090385 phagosome-lysosome fusion
GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome
GO:0099003 vesicle-mediated transport in synapse
GO:0099638 endosome to plasma membrane protein transport
GO:1903542 negative regulation of exosomal secretion
GO:1903543 positive regulation of exosomal secretion
GO:1905366 negative regulation of intralumenal vesicle formation
Cellular Component
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005794 Golgi apparatus
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030667 secretory granule membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0030904 retromer complex
GO:0031902 late endosome membrane
GO:0031966 mitochondrial membrane
GO:0033162 melanosome membrane
GO:0034045 phagophore assembly site membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0045335 phagocytic vesicle
GO:0070062 extracellular exosome
GO:0097208 alveolar lamellar body
GO:0098588 bounding membrane of organelle
GO:0098830 presynaptic endosome
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:6iyb, PDBe:6iyb, PDBj:6iyb
PDBsum6iyb
PubMed30721249
UniProtP51149|RAB7A_HUMAN Ras-related protein Rab-7a (Gene Name=RAB7A)

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