Structure of PDB 7vcv Chain E Binding Site BS01

Receptor Information

>7vcv Chain E (length=758) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKG
KKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYG
KRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAV
EFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRK
QLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE
TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAP
KREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG
RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADL
AALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNP
SALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS
KGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVRE
IFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGM
STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANL
RKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRER
ERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQT
LQQSRGFG

Ligand information

Ligand ID

AGS

InChI

InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1

InChIKey

NLTUCYMLOPLUHL-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01	O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O

Formula

C10 H16 N5 O12 P3 S

Name

PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE

PDB chain

7vcv Chain F Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7vcv Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state.
Resolution	3.21 Å
Binding residue (original residue number in PDB)	R635 R766
Binding residue (residue number reindexed from 1)	R624 R755
Annotation score	4

Enzymatic activity

Enzyme Commision number

3.6.4.6: vesicle-fusing ATPase.

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008289	lipid binding
GO:0016787	hydrolase activity
GO:0016887	ATP hydrolysis activity
GO:0019903	protein phosphatase binding
GO:0019904	protein domain specific binding
GO:0031593	polyubiquitin modification-dependent protein binding
GO:0031625	ubiquitin protein ligase binding
GO:0035800	deubiquitinase activator activity
GO:0036435	K48-linked polyubiquitin modification-dependent protein binding
GO:0042288	MHC class I protein binding
GO:0042802	identical protein binding
GO:0043531	ADP binding
GO:0044389	ubiquitin-like protein ligase binding
GO:0044877	protein-containing complex binding
GO:0140036	ubiquitin-modified protein reader activity
GO:1904288	BAT3 complex binding
GO:1990381	ubiquitin-specific protease binding

	Biological Process
GO:0006281	DNA repair
GO:0006302	double-strand break repair
GO:0006511	ubiquitin-dependent protein catabolic process
GO:0006734	NADH metabolic process
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006914	autophagy
GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0006974	DNA damage response
GO:0010498	proteasomal protein catabolic process
GO:0010918	positive regulation of mitochondrial membrane potential
GO:0016236	macroautophagy
GO:0016567	protein ubiquitination
GO:0019079	viral genome replication
GO:0019985	translesion synthesis
GO:0030968	endoplasmic reticulum unfolded protein response
GO:0030970	retrograde protein transport, ER to cytosol
GO:0031334	positive regulation of protein-containing complex assembly
GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032510	endosome to lysosome transport via multivesicular body sorting pathway
GO:0033554	cellular response to stress
GO:0034605	cellular response to heat
GO:0035331	negative regulation of hippo signaling
GO:0035617	stress granule disassembly
GO:0036297	interstrand cross-link repair
GO:0036503	ERAD pathway
GO:0042981	regulation of apoptotic process
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045184	establishment of protein localization
GO:0045732	positive regulation of protein catabolic process
GO:0045879	negative regulation of smoothened signaling pathway
GO:0046034	ATP metabolic process
GO:0050807	regulation of synapse organization
GO:0051228	mitotic spindle disassembly
GO:0061857	endoplasmic reticulum stress-induced pre-emptive quality control
GO:0070842	aggresome assembly
GO:0071218	cellular response to misfolded protein
GO:0072389	flavin adenine dinucleotide catabolic process
GO:0090263	positive regulation of canonical Wnt signaling pathway
GO:0097352	autophagosome maturation
GO:0106300	protein-DNA covalent cross-linking repair
GO:0120186	negative regulation of protein localization to chromatin
GO:0140455	cytoplasm protein quality control
GO:1901224	positive regulation of non-canonical NF-kappaB signal transduction
GO:1903006	positive regulation of protein K63-linked deubiquitination
GO:1903007	positive regulation of Lys63-specific deubiquitinase activity
GO:1903715	regulation of aerobic respiration
GO:1903843	cellular response to arsenite ion
GO:1903862	positive regulation of oxidative phosphorylation
GO:1905634	regulation of protein localization to chromatin
GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process
GO:2001171	positive regulation of ATP biosynthetic process

	Cellular Component
GO:0000502	proteasome complex
GO:0005576	extracellular region
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005783	endoplasmic reticulum
GO:0005789	endoplasmic reticulum membrane
GO:0005811	lipid droplet
GO:0005829	cytosol
GO:0010494	cytoplasmic stress granule
GO:0032991	protein-containing complex
GO:0034098	VCP-NPL4-UFD1 AAA ATPase complex
GO:0034774	secretory granule lumen
GO:0035578	azurophil granule lumen
GO:0035861	site of double-strand break
GO:0036513	Derlin-1 retrotranslocation complex
GO:0043231	intracellular membrane-bounded organelle
GO:0045202	synapse
GO:0048471	perinuclear region of cytoplasm
GO:0070062	extracellular exosome
GO:0098978	glutamatergic synapse
GO:1904813	ficolin-1-rich granule lumen
GO:1904949	ATPase complex
GO:1990730	VCP-NSFL1C complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7vcv, PDBe:7vcv, PDBj:7vcv
PDBsum	7vcv
PubMed	35190543
UniProt	P55072\|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

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