Structure of PDB 8zq3 Chain A Binding Site BS01

Receptor Information

>8zq3 Chain A (length=179) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDR
LVTMQIWDTAGLERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDE
FLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETS
AKEAINVEQAFQTIARNALKQETEVELYN

Ligand information

Ligand ID

GDP

InChI

InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

8zq3 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	8zq3 Structure of GDP-bound Rab7 Q67L in complex with ORP1L.
Resolution	2.43 Å
Binding residue (original residue number in PDB)	S17 G18 V19 G20 K21 T22 S23 F33 N35 N125 K126 D128 L129 S155 A156 K157
Binding residue (residue number reindexed from 1)	S12 G13 V14 G15 K16 T17 S18 F28 N30 N120 K121 D123 L124 S150 A151 K152
Annotation score	4

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:8zq3, PDBe:8zq3, PDBj:8zq3
PDBsum	8zq3
PubMed	38897042
UniProt	P51149\|RAB7A_HUMAN Ras-related protein Rab-7a (Gene Name=RAB7A)

[Back to BioLiP]