4LDT - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE STRUCTURE OF H/CEOTUB1-UBIQUITIN ALDEHYDE-UBCH5B~UB

Authors :   R. Wiener, A. T. Dibello, P. M. Lombardi, C. M. Guzzo, X. Zhang, M. J. Matu C. Wolberger

Date :   25 Jun 13 (Deposition) - 14 Aug 13 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Isopeptidase, Ubiquitin-Conjugating, Post-Translational Modification, Ubiquitin, Ubiquitin-Aldehyde, Hydrolase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Wiener, A. T. Dibello, P. M. Lombardi, C. M. Guzzo, X. Zhang, M. J. Matunis, C. Wolberger
E2 Ubiquitin-Conjugating Enzymes Regulate The Deubiquitinating Activity Of Otub1.
Nat. Struct. Mol. Biol. V. 20 1033 2013
PubMed-ID: 23955022 | Reference-DOI: 10.1038/NSMB.2655

Molecule 1 - UBIQUITIN THIOESTERASE OTUBAIN-LIKE
	Chains	:	A
	EC Number	:	3.4.19.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SEE REMARK 999
	Gene	:	OTUB1, OTB1, OTU1, HSPC263, C25D7.8, OTUB-1
	Organism Common	:	HUMAN, NEMATODE
	Organism Scientific	:	HOMO SAPIENS, CAENORHABDITIS ELEGANS
	Organism Taxid	:	9606, 6239
	Synonym	:	DEUBIQUITINATING ENZYME OTUB1, OTU DOMAIN-CONTAINING UBIQUITIN ALDEHYDE-BINDING PROTEIN 1, OTUBAIN-1, HOTU1, UBIQUITIN- SPECIFIC-PROCESSING PROTEASE OTUB1, DEUBIQUITINATING ENZYME OTUBAIN- LIKE, UBIQUITIN-SPECIFIC-PROCESSING PROTEASE OTUBAIN-LIKE

Molecule 2 - UBIQUITIN ALDEHYDE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - UBIQUITIN-CONJUGATING ENZYME E2 D2
	Chains	:	C
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITIN CARRIER PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, UBIQUITIN- PROTEIN LIGASE D2, P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1

Molecule 4 - UBIQUITIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	UBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GLZ	1	Mod. Amino Acid	AMINO-ACETALDEHYDE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:101 , LEU A:102 , ARG A:105 , ILE A:146	BINDING SITE FOR RESIDUE EDO A 301
2	AC2	SOFTWARE	ALA A:155 , THR A:158 , HOH A:492	BINDING SITE FOR RESIDUE EDO A 302
3	AC3	SOFTWARE	ILE A:192 , ASP A:193 , GLU A:194 , TYR A:201 , ASP A:214 , LEU A:216 , HOH A:450 , HOH A:482	BINDING SITE FOR RESIDUE EDO A 303
4	AC4	SOFTWARE	ASP B:32 , HOH B:220 , HOH B:221 , HOH B:222 , HOH B:227	BINDING SITE FOR RESIDUE MG B 101
5	AC5	SOFTWARE	MET C:38 , GLY C:39 , GLN C:46 , GLY C:47 , GLY C:48	BINDING SITE FOR RESIDUE EDO C 201

(no "SS Bond" information available for 4LDT)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:248	-	Pro A:249
2	Tyr C:60	-	Pro C:61

(no "SAP(SNP)/Variant" information available for 4LDT)

(no "PROSITE Motif" information available for 4LDT)

(no "Exon" information available for 4LDT)

Asymmetric/Biological 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhh.....hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhhhhh...eeeee..........eeeee........eeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldt A  19 CLAYDEAIMAQQDRIQQEIAVQNPLVATLAPFSILCAEYDNETSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSRDWTRTLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLITSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAPNGGWHYDIPSDQIAPEITLLYRPGHYDVIYKKD 275
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  ||   260       270     
                                                                                                                                                                                                                                                                  251|                     
                                                                                                                                                                                                                                                                   254

Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains d4ldtb_ B: Ubiquitin                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4ldt B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGg  76
                                    10        20        30        40        50        60        70     |
                                                                                                      76-GLZ

Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4ldtc_ C: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldt C   0 GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain D from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains d4ldtd_ D: Ubiquitin                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4ldt D   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: Ubiquitin (162)

Human (Homo sapiens) [TaxId: 9606] (121)

1a	d4ldtb_	B:
1b	d4ldtd_	D:

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: UBC-related (135)

Protein domain: automated matches (40)

Human (Homo sapiens) [TaxId: 9606] (25)

d4ldtc_

(no "CATH Domain" information available for 4LDT)

(no "Pfam Domain" information available for 4LDT)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological 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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLZ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 ]

	Cis Peptide Bonds
		Ile A:248 - Pro A:249	[ RasMol ]
		Tyr C:60 - Pro C:61	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4ldt
		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
	OTUB1_HUMAN \| Q96FW1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	OTUBL_CAEEL \| Q9XVR6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	UB2D2_HUMAN \| P62837
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	UBC_HUMAN \| P0CG48
		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)
	3.4.19.12
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	6.3.2.19
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	OTUB1_HUMAN \| Q96FW1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	OTUBL_CAEEL \| Q9XVR6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	UB2D2_HUMAN \| P62837
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	UBC_HUMAN \| P0CG48
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 4LDT)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (111, 137)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File