3NIS - JenaLib

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:123 , CYS A:148 , CYS A:151 , CYS A:175	BINDING SITE FOR RESIDUE ZN A 1
02	AC2	SOFTWARE	HIS A:118 , CYS A:151 , CYS A:177 , CYS A:189	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	CYS A:136 , CYS A:139 , HIS A:157 , HIS A:160	BINDING SITE FOR RESIDUE ZN A 3
04	AC4	SOFTWARE	ILE A:129 , GLU A:169	BINDING SITE FOR RESIDUE ACT A 195
05	AC5	SOFTWARE	CYS B:123 , CYS B:148 , CYS B:151 , CYS B:175	BINDING SITE FOR RESIDUE ZN B 1
06	AC6	SOFTWARE	HIS B:118 , CYS B:151 , CYS B:177 , CYS B:189	BINDING SITE FOR RESIDUE ZN B 2
07	AC7	SOFTWARE	CYS B:136 , CYS B:139 , HIS B:157 , HIS B:160	BINDING SITE FOR RESIDUE ZN B 3
08	AC8	SOFTWARE	ILE B:166	BINDING SITE FOR RESIDUE ACT B 195
09	AC9	SOFTWARE	CYS D:123 , CYS D:148 , CYS D:151 , CYS D:175	BINDING SITE FOR RESIDUE ZN D 1
10	BC1	SOFTWARE	HIS D:118 , CYS D:151 , CYS D:177 , CYS D:189	BINDING SITE FOR RESIDUE ZN D 2
11	BC2	SOFTWARE	CYS D:136 , CYS D:139 , HIS D:157 , HIS D:160	BINDING SITE FOR RESIDUE ZN D 3
12	BC3	SOFTWARE	CYS F:123 , CYS F:148 , CYS F:151 , CYS F:175	BINDING SITE FOR RESIDUE ZN F 1
13	BC4	SOFTWARE	HIS F:118 , CYS F:151 , CYS F:177 , CYS F:189	BINDING SITE FOR RESIDUE ZN F 2
14	BC5	SOFTWARE	CYS F:136 , CYS F:139 , HIS F:157 , HIS F:160	BINDING SITE FOR RESIDUE ZN F 3
15	BC6	SOFTWARE	GLN B:194 , HOH F:60 , THR F:144 , VAL F:146 , GLY F:173 , ILE F:174 , ASP F:176	BINDING SITE FOR RESIDUE ACT F 195

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:82
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:82
                                   122       132       142       152       162       172       182       192  
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee................hhhhhh...eeeee....eee.....hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: A:121-194 UniProt: 121-194                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3nis A 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
                                   122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:82
                                   122       132       142       152       162       172       182       192  
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...............eeeee................hhhhhh...eeeee............hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: B:121-194 UniProt: 121-194                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3nis B 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
                                   122       132       142       152       162       172       182       192

Chain D from PDB  Type:PROTEIN  Length:81
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:81
                                   122       132       142       152       162       172       182       192 
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee................hhhhhh...eeeee............hhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: D:121-193 UniProt: 121-194                                   PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 3nis D 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 193
                                   122       132       142       152       162       172       182       192

Chain F from PDB  Type:PROTEIN  Length:82
 aligned with UBR1_YEAST | P19812 from UniProtKB/Swiss-Prot  Length:1950

    Alignment length:82
                                   122       132       142       152       162       172       182       192  
           UBR1_YEAST   113 GDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------zf-UBR-3nisF01 F:121-193                                                 - Pfam domains (1)
           Pfam domains (2) --------zf-UBR-3nisF02 F:121-193                                                 - Pfam domains (2)
           Pfam domains (3) --------zf-UBR-3nisF03 F:121-193                                                 - Pfam domains (3)
           Pfam domains (4) --------zf-UBR-3nisF04 F:121-193                                                 - Pfam domains (4)
         Sec.struct. author hhhhh..............eeeee................hhhhhh...eeeee............hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ZF_UBR  PDB: F:121-194 UniProt: 121-194                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 3nis F 113 GSVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQ 194
                                   122       132       142       152       162       172       182       192

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (17, 17)

Asymmetric Unit(hide GO term definitions)

Chain A,B,D,F (UBR1_YEAST | P19812)

molecular function
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006513	protein monoubiquitination	Addition of a single ubiquitin group to a protein.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0090089	regulation of dipeptide transport	Any process that modulates the rate, frequency or extent of dipeptide transport. Dipeptide transport is the directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:1990116	ribosome-associated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide encoded by an aberrant message and associated with a stalled ribosome. Degradation is initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the ribosome-associated protein.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
	GO:0071629	ubiquitin-dependent catabolism of misfolded proteins by cytoplasm-associated proteasome	The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the cytoplasm, which are targeted to cytoplasmic proteasomes for degradation.
	GO:0071596	ubiquitin-dependent protein catabolic process via the N-end rule pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the N-end rule pathway. In the N-end rule pathway, destabilizing N-terminal residues (N-degrons) in substrates are recognized by E3 ligases (N-recognins), whereupon the substrates are linked to ubiquitin and then delivered to the proteasome for degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0008540	proteasome regulatory particle, base subcomplex	The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.
	GO:0000151	ubiquitin ligase complex	A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nis)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3nis
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	UBR1_YEAST \| P19812
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (15, 15)