Structure of PDB 7mex Chain A Binding Site BS03

Receptor Information

>7mex Chain A (length=1737) Species: 559292 (Saccharomyces cerevisiae S288C)

GSLQGHIRRTLRSIHNLPYFRYTRGPTERADMSRALKEFIYRYLYFVISN
SGENLPTLFNAHPKQKLLTVFPDSLEDAVDIDKITSQQTIPFYKIDESRI
GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHV
CTDICTEFTSGICDCGDEEAWNSPLHCKAEEQEDVWNDSVNIALVELVLA
EVFDYFIDVFNQNIEPLPTIQKDITIKLREMTQQGKMYERAQFLNDLKYE
NDYMFDKIDPENYTVIIYNDEYHNYSQATTALRQGVPDNVHIDLLTSRID
GEGRAMLKCSQDLSSVLGGFFAVQTNGLSATLTSWSEYLHQETCKYIILW
ITHCLNIPNSSFQTTFRNMMGKTLCSEYLNATECRDMTPVVEKYFSNKFD
KNDPYRYIDLSILADGNQIPLGHHKILPESSTHSLSPLINDVETPTSRTY
SNTRLQHILYFDNRYWKRLRKDIQNVIIPTLASSNLYKPIFCQQVVEIFN
HITRSVAYMDREPQLTAIRECVVQLFTCPTNAKNIFENQSFLDIVWSIID
IFKEFCKVEGGVLIWQRVQKSNLTKSYSISFKQGLYTVETLLSKVHDPNI
PLRPKEIISLLTLCKLFNGAWKIKRKEGEHVLHEDQNFISYLEYTTSIYS
IIQTAEKVSEKSKDSIDSKLFLNAIRIISSFLGNRSLTYKLIYDSHEVIK
FSVSHERVAFMNPLQTMLSFLIEKVSLKDAYEALEDCSDFLKISDFSLRS
VVLCSQIDVGFWVRNGMSVLHQASYYKNNPELGSYSRDIHLNQLAILWER
DDIPRIIYNILDRWELLDWFTGEVDYQHTVYEDKISFIIQQFIAFIYQIL
TERQYFKTFSSLKDRRMDQIKNSIIYNLYMKPLSYSKLLRSVPDYLTEDT
TEFDEALEEVSVFVEPKGLADNGVFKLKASLYAKVDPLKLLNLENEFESS
ATIIKSHLAKDKDEIAKVVLIPQVSIKQLDKDALNLGAFTRNTVFAKVVY
KLLQVCLDMEDSTFLNELLHLVHGIFRDDELINGKDSIPEAYLSKPICNL
LLSIANAKSDVFSESIVRKADYLLEKMIMKKPNELFESLIASFGNQYVND
YKDKKLRTEKERKRRLAKKHQARLLAKFNNQQTKFMKEHESEFTCALCQD
SSSTDFFVIPAYHDHSPIFRPGNIFNPNEFMPMWDGFYNDDEKQAYIDDD
VLEALKENGSCGSRKVFVSCNHHIHHNCFKRYVQKKRFSSNAFICPLCQT
FSNCTLPLCQTSKANTGLSLDMFLESELSLDTLSRLFKPFTEENYRTINS
IFSLMISQCQGFDKAVRKRANFSHKDVSLILSVHWANTISMLEIASRLEK
PYSISFFRSREQKYKTLKNILVCIMLFTFVIGKPSMEFEPYPQQPDTVWN
QNQLFQYIVRSALFSPVSLRQTVTEALTTFSRQFLRDFLQGLSDAEQVTK
LYAKASKIGDVLKVSEQMLFALRTISDVRMEGLDSESIIYDLAYTFLLKS
LLPTIRRCLVFIKVLHELVKDSENETLVINGHEVEEELEFEDTAEFVNKA
LKMITEKESLVDLLTTQESIVSHPYLENIPYEYCGIIKLIDLSKYLNTYV
TQSKEIKLREERSQHMKNADNRLDFKICLTCGVKVHLRADRHEMTKHLNK
NCFKPFGAFLMPNSSEVCLHLTQPPSNIFISAPYLNSHGEVGRNAMRRGD
LTTLNLKRYEHLNRLWINNEIPGYISRVMGDEFRVTI

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 7mex Chain A Residue 2002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mex Structural insights into Ubr1-mediated N-degron polyubiquitination.
• Resolution: 3.35 Å
• Binding residue (original residue number in PDB): C123 C151 C175
• Binding residue (residue number reindexed from 1): C111 C139 C163
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

Gene Ontology

Molecular Function

• GO:0004842 ubiquitin-protein transferase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding
• GO:0061630 ubiquitin protein ligase activity
• GO:1904855 proteasome regulatory particle binding

Biological Process

• GO:0000209 protein polyubiquitination
• GO:0006513 protein monoubiquitination
• GO:0016567 protein ubiquitination
• GO:0034620 cellular response to unfolded protein
• GO:0036503 ERAD pathway
• GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway
• GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
• GO:0072671 mitochondria-associated ubiquitin-dependent protein catabolic process
• GO:0090089 regulation of dipeptide transport
• GO:0120174 stress-induced homeostatically regulated protein degradation pathway
• GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process

Cellular Component

• GO:0000151 ubiquitin ligase complex
• GO:0005737 cytoplasm
• GO:0008540 proteasome regulatory particle, base subcomplex
• GO:1990303 UBR1-RAD6 ubiquitin ligase complex

External links

• PDB: RCSB:7mex, PDBe:7mex, PDBj:7mex
• PDBsum: 7mex
• PubMed: 34789879
• UniProt: P19812|UBR1_YEAST E3 ubiquitin-protein ligase UBR1 (Gene Name=UBR1)