4MDK - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CDC34-UBIQUITIN-CC0651 COMPLEX

Authors :   D. F. Ceccarelli, S. Orlicky, M. Tyers, F. Sicheri

Date :   22 Aug 13 (Deposition) - 11 Dec 13 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.61

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E  (1x)
Biol. Unit 2: B,F  (1x)
Biol. Unit 3: C,G  (1x)
Biol. Unit 4: D,H  (1x)

Keywords :   Ubiquitin Conjugating Enzyme Domain, E2 Ligase Inhibitor, Ligase- Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Huang, D. F. Ceccarelli, S. Orlicky, D. J. St-Cyr, A. Ziemba, P. Garg S. Plamondon, M. Auer, S. Sidhu, A. Marinier, G. Kleiger, M. Tyers, F. Sicheri
E2 Enzyme Inhibition By Stabilization Of A Low-Affinity Interface With Ubiquitin.
Nat. Chem. Biol. V. 10 156 2014
PubMed-ID: 24316736 | Reference-DOI: 10.1038/NCHEMBIO.1412

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 R1
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PROEX
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	E2 DOMAIN (UNP RESIDUES 7-184)
	Gene	:	CDC34, UBCH3, UBE2R1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITIN-CONJUGATING ENZYME E2-32 KDA COMPLEMENTING, UBIQUITIN-CONJUGATING ENZYME E2-CDC34, UBIQUITIN-PROTEIN LIGASE R1

Molecule 2 - UBIQUITIN
	Chains	:	E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 76-152
	Gene	:	UBC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A				E
Biological Unit 2 (1x)	:		B				F
Biological Unit 3 (1x)	:			C				G
Biological Unit 4 (1x)	:				D				H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	U94	4	Ligand/Ion	4,5-DIDEOXY-5-(3',5'-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	U94	1	Ligand/Ion	4,5-DIDEOXY-5-(3',5'-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	U94	1	Ligand/Ion	4,5-DIDEOXY-5-(3',5'-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	U94	1	Ligand/Ion	4,5-DIDEOXY-5-(3',5'-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC ACID

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	U94	1	Ligand/Ion	4,5-DIDEOXY-5-(3',5'-DICHLOROBIPHENYL-4-YL)-4-[(METHOXYACETYL)AMINO]-L-ARABINONIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:48 , THR A:51 , TYR A:52 , TYR A:53 , PHE A:58 , LEU A:131 , ASN A:132 , TYR A:148 , TRP A:151 , TYR A:161 , GLY E:47	BINDING SITE FOR RESIDUE U94 A 201
2	AC2	SOFTWARE	PHE B:46 , PRO B:48 , THR B:51 , TYR B:52 , TYR B:53 , PHE B:58 , LEU B:131 , ASN B:132 , TRP B:151 , GLY F:47	BINDING SITE FOR RESIDUE U94 B 201
3	AC3	SOFTWARE	PRO C:48 , THR C:51 , TYR C:52 , TYR C:53 , PHE C:58 , LEU C:131 , ASN C:132 , TRP C:151 , HOH C:306 , GLY G:47	BINDING SITE FOR RESIDUE U94 C 201
4	AC4	SOFTWARE	ILE D:45 , PHE D:46 , PRO D:48 , ASN D:50 , THR D:51 , TYR D:52 , TYR D:53 , PHE D:58 , LEU D:131 , ASN D:132 , TRP D:151 , HOH D:307 , GLY H:47	BINDING SITE FOR RESIDUE U94 D 201

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

Asymmetric Unit

No.	Residues
1	Tyr A:68	-	Pro A:69
2	Glu B:35	-	Gly B:36
3	Tyr B:68	-	Pro B:69
4	Tyr C:68	-	Pro C:69
5	Tyr D:68	-	Pro D:69
6	Met H:-1	-	Gly H:0

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

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

(no "Exon" information available for 4MDK)

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:168
                                                                                                                                                                                                        
               SCOP domains d4mdka_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeeee.......eeeeeee..........eeeeeee..........eeee................hhhhh..........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mdk A   7 PSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCISILHPPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVP 184
                                    16        26        36        46        56        66        76        86        96  ||   116       126       136       146       156       166       176        
                                                                                                                       99|                                                                          
                                                                                                                       110

Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains d4mdkb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee.......eeeeeee..........eeeeeee..........eeee........................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdk B   7 PSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCISIWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVP 184
                                    16        26        36        46        56        66        76        86        96|      123       133       143       153       163       173       183 
                                                                                                                    96|                                                                      
                                                                                                                    114

Chain C from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains d4mdkc_ C: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee.......eeeeeee..........eeeeeee..........eeee................hhhhh..........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mdk C   7 PSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCISILHPPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVP 184
                                    16        26        36        46        56        66        76        86        96   ||  116       126       136       146       156       166       176        
                                                                                                                       100|                                                                         
                                                                                                                        111

Chain D from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains d4mdkd_ D: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee.......eeeeeee..........eeeeeee..........eeee....................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdk D   7 PSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCNPTQNVRTILLSVISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAERDGVKVP 184
                                    16        26        36        46        56        66        76        86      |117       127       137       147       157       167       177       
                                                                                                                 93|                                                                     
                                                                                                                 115

Chain E from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains d4mdke_ E: Ubiquitin                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4mdk E  -1 MGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  74
                                     8        18        28        38        48        58        68

Chain F from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains d4mdkf_ F: Ubiquitin                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4mdk F  -1 MGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  74
                                     8        18        28        38        48        58        68

Chain G from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains d4mdkg_ G: Ubiquitin                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee......hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4mdk G   2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR  74
                                    11        21        31        41        51        61        71

Chain H from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains d4mdkh_ H: Ubiquitin                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4mdk H  -1 MGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR  72
                                     8        18        28        38        48        58        68

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 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	d4mdke_	E:
1b	d4mdkf_	F:
1c	d4mdkg_	G:
1d	d4mdkh_	H:

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: automated matches (16)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (10)

2a	d4mdka_	A:
2b	d4mdkb_	B:
2c	d4mdkc_	C:
2d	d4mdkd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

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
		U94	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:35 - Gly B:36	[ RasMol ]
		Met H:-1 - Gly H:0	[ RasMol ]
		Tyr A:68 - Pro A:69	[ RasMol ]
		Tyr B:68 - Pro B:69	[ RasMol ]
		Tyr C:68 - Pro C:69	[ RasMol ]
		Tyr D:68 - Pro D:69	[ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	4mdk
		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
	UB2R1_HUMAN \| P49427
		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)
	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
	UB2R1_HUMAN \| P49427
		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 4MDK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (99, 105)

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