Structure of PDB 3cf1 Chain C Binding Site BS03

Receptor Information

>3cf1 Chain C (length=723) Species: 10090 (Mus musculus)

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

Ligand information

• Ligand ID: AF3
• InChI: InChI=1S/Al.3FH/h;3*1H/q+3;;;/p-3
• InChIKey: KLZUFWVZNOTSEM-UHFFFAOYSA-K
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: F[Al](F)F
• Formula: Al F3
• Name: ALUMINUM FLUORIDE
• PDB chain: 3cf1 Chain C Residue 915

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3cf1 Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
• Resolution: 4.4 Å
• Binding residue (original residue number in PDB): P520 G521 C522 G523 K524
• Binding residue (residue number reindexed from 1): P500 G501 C502 G503 K504
• Annotation score: 1

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: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: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: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:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
• 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: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: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:0035861 site of double-strand break
• GO:0036513 Derlin-1 retrotranslocation complex
• GO:0043209 myelin sheath
• GO:0045202 synapse
• GO:0048471 perinuclear region of cytoplasm
• GO:0098978 glutamatergic synapse
• GO:1904949 ATPase complex
• GO:1990730 VCP-NSFL1C complex

External links

• PDB: RCSB:3cf1, PDBe:3cf1, PDBj:3cf1
• PDBsum: 3cf1
• PubMed: 18462676
• UniProt: Q01853|TERA_MOUSE Transitional endoplasmic reticulum ATPase (Gene Name=Vcp)