Structure of PDB 5ftm Chain F Binding Site BS02

Receptor Information

>5ftm Chain F (length=728) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

NRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCI
VLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDP
SPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMV
ELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN
GPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV
ERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIG
IPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVE
VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPP
GCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAA
PCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFII
GATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV
DLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIVPEIRRDHFEEAM
RFARRSVSDNDIRKYEMFAQTLQQSRGF

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

5ftm Chain F Residue 901 [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	5ftm 2.3 A Resolution Cryo-Em Structure of Human P97 and Mechanism of Allosteric Inhibition
Resolution	3.2 Å
Binding residue (original residue number in PDB)	I479 G480 P520 G521 C522 G523 K524 T525 L526 N624 G684 A685
Binding residue (residue number reindexed from 1)	I459 G460 P500 G501 C502 G503 K504 T505 L506 N604 G664 A665
Annotation score	4

Enzymatic activity

Catalytic site (original residue number in PDB)	K251 T252 D304 N348 R453 K524 T525 D577 E578 D609 A685
Catalytic site (residue number reindexed from 1)	K231 T232 D284 N328 R433 K504 T505 D557 E558 D589 A665
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:5ftm, PDBe:5ftm, PDBj:5ftm
PDBsum	5ftm
PubMed	26822609
UniProt	P55072\|TERA_HUMAN Transitional endoplasmic reticulum ATPase (Gene Name=VCP)

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