5D1K - JenaLib

Title :   CRYSTAL STRUCTURE OF UBCH5B IN COMPLEX WITH THE RING-U5BR FRAGMENT OF AO7

Authors :   Y. -H. Liang, S. Li, A. M. Weissman, X. Ji

Date :   08 Oct 13 (Deposition) - 28 Oct 15 (Release) - 30 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

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

Keywords :   Ubiquitin Conjugating Enzyme (E2), Ubiquitin Ligase (E3), Ring Finger, Ubiquitination, Ubiquitin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Li, Y. H. Liang, J. Mariano, M. B. Metzger, D. K. Stringer, V. A. Hristova, J. Li, P. A. Randazzo, Y. C. Tsai, X. Ji, A. M. Weissman
Insights Into Ubiquitination From The Unique Clamp-Like Binding Of The Ring E3 Ao7 To The E2 Ubch5B.
J. Biol. Chem. V. 290 30225 2015
PubMed-ID: 26475854 | Reference-DOI: 10.1074/JBC.M115.685867

Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
	Chains	:	A
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
	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 2 - E3 UBIQUITIN-PROTEIN LIGASE RNF25
	Chains	:	B
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 126-258
	Gene	:	RNF25
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RING FINGER PROTEIN 25

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:137 , TRP A:141 , OXL A:203	binding site for residue EDO A 201
2	AC2	SOFTWARE	ARG A:72 , SER A:80 , TRP A:141 , TYR A:145 , OXL A:203	binding site for residue PEG A 202
3	AC3	SOFTWARE	TRP A:141 , LYS A:144 , TYR A:145 , EDO A:201 , PEG A:202 , HOH A:301	binding site for residue OXL A 203
4	AC4	SOFTWARE	CYS B:135 , CYS B:138 , HIS B:158 , CYS B:161	binding site for residue ZN B 301
5	AC5	SOFTWARE	CYS B:153 , HIS B:155 , CYS B:198 , CYS B:201	binding site for residue ZN B 302
6	AC6	SOFTWARE	THR B:149 , LYS B:150 , THR B:151 , PRO B:152 , VAL B:206 , GLU B:247 , ARG B:248	binding site for residue EDO B 303
7	AC7	SOFTWARE	ASN A:41 , GLN A:46 , MET A:147 , LYS B:150 , TYR B:154 , ARG B:248	binding site for residue EDO B 304

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
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Chain A from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeeee..eeeeeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1k A   2 ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee.....eeehhhhhhhhhhhhhhhhh...............hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5d1k B 129 NIPHGQCVICLYGFQEKEAFTKTPCYHYFHCHCLARYIQHMEQELKAQGGVQCPVCREPLVYDLASLKAAPEPQQPMELYQPSAESLRQQEERKRLYQRQQERGGIIDLE 255
                                   138       148       158       168       195       205       215       225       235       245       255
                                                                          177|                                                            
                                                                           195

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (29, 32)

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		Tyr A:60 - Pro A:61	[ RasMol ]

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Description