3B76 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF HUMAN LIGAND-OF-NUMB PROTEIN-X (LNX1) IN COMPLEX WITH THE C-TERMINAL PEPTIDE FROM THE COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR

Authors :   E. Ugochukwu, N. Burgess-Brown, G. Berridge, J. Elkins, G. Bunkoczi, A. C. W. Pike, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards O. Gileadi, F. Von Delft, D. Doyle, Structural Genomics Consortiu

Date :   30 Oct 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Pdz, Bound Ligand, Structural Genomics, Structural Genomics Consortium, Sgc, Ligase, Metal-Binding, Ubl Conjugation Pathway, Zinc-Finger, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, N. Burgess-Brown, G. Berridge, J. Elkins, G. Bunkoczi, A. C. W. Pike, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards O. Gileadi, F. Von Delft, D. Doyle
Crystal Structure Of The Third Pdz Domain Of Human Ligand-Of-Numb Protein-X (Lnx1) In Complex With The C-Terminal Peptide From The Coxsackievirus And Adenovirus Receptor.
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (4, 8)

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.9a	ENST00000263925	9a	ENSE00002073967	chr4:54457783-54457555	229	LNX1_HUMAN	-	0	0	-	-
1.10g	ENST00000263925	10g	ENSE00001126725	chr4:54440255-54439790	466	LNX1_HUMAN	1-127	127	0	-	-
1.12b	ENST00000263925	12b	ENSE00000341408	chr4:54374394-54374153	242	LNX1_HUMAN	127-208	82	0	-	-
1.13	ENST00000263925	13	ENSE00000715376	chr4:54373636-54373484	153	LNX1_HUMAN	208-259	52	0	-	-
1.14b	ENST00000263925	14b	ENSE00000877896	chr4:54365010-54364808	203	LNX1_HUMAN	259-326	68	0	-	-
1.15	ENST00000263925	15	ENSE00000969364	chr4:54362561-54362190	372	LNX1_HUMAN	327-450	124	0	-	-
1.16	ENST00000263925	16	ENSE00000969365	chr4:54348021-54347887	135	LNX1_HUMAN	451-495	45	2	A:402-406 B:401-406	5 6
1.17	ENST00000263925	17	ENSE00000969366	chr4:54344909-54344732	178	LNX1_HUMAN	496-555	60	2	A:407-459 B:407-459	53 53
1.18	ENST00000263925	18	ENSE00000969367	chr4:54343148-54342920	229	LNX1_HUMAN	555-631	77	2	A:459-498 B:459-498	40 40
1.19	ENST00000263925	19	ENSE00000969368	chr4:54327760-54327602	159	LNX1_HUMAN	631-684	54	2	A:499-502 (gaps) B:499-502 (gaps)	26 26
1.20a	ENST00000263925	20a	ENSE00001488463	chr4:54327209-54326623	587	LNX1_HUMAN	684-728	45	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 =
	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:101
 aligned with LNX1_HUMAN | Q8TBB1 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:202
                                   480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670  
           LNX1_HUMAN   471 IFQEAGWNSNGSWSPGPGERSNTPKPLHPTITCHEKVVNIQKDPGESLGMTVAGGASHREWDLPIYVISVEPGGVISRDGRIKTGDILLNVDGVELTEVSRSEAVALLKRTSSSIVLKALEVKEYEPQEDCSSPAALDSNHNMAPPSDWSPSWVMWLELPRCLYNCKDIVLRRNTAGSLGFCIVGGYEEYNGNKPFFIKSIV 672
               SCOP domains d3b76                           a_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 3b76A                           00 A:402-502  [code=2.30.42.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee---------------------------eeeeeeeee........eeeee..........eeeeee...hhhhhhh......eeeee..ee.hhhhhhhhhhhhhh...eeeeeeeeeee----------------------------------------------------.----------------------eee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PDZ  PDB: A:411-497 UniProt: 507-593                                                   --------------------------------------------PDZ  PDB: A:499-502                 PROSITE
           Transcript 1 (1) Exon 1.16  PDB: A:402-406Exon 1.17  PDB: A:407-459 UniProt: 496-555 [INCOMPLETE]     ---------------------------------------------------------------------------Exon 1.19  PDB: A:499-502 (gaps)           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.18  PDB: A:459-498 UniProt: 555-631 [INCOMPLETE]                      ----------------------------------------- Transcript 1 (2)
                 3b76 A 402 LYFQS---------------------------MHEKVVNIQKDPGESLGMTVAGGASHREWDLPIYVISVEPGGVISRDGRIKTGDILLNVDGVELTEVSRSEAVALLKRTSSSIVLKALEVKE----------------------------------------------------G----------------------SIV 502
                                |    -         -         -  |    414       424       434       444       454       464       474       484       494   |     -         -         -         -         -      |  -         -       500  
                              406                         407                                                                                        498                                                  499                    500

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with LNX1_HUMAN | Q8TBB1 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:203
                                   479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669   
           LNX1_HUMAN   470 DIFQEAGWNSNGSWSPGPGERSNTPKPLHPTITCHEKVVNIQKDPGESLGMTVAGGASHREWDLPIYVISVEPGGVISRDGRIKTGDILLNVDGVELTEVSRSEAVALLKRTSSSIVLKALEVKEYEPQEDCSSPAALDSNHNMAPPSDWSPSWVMWLELPRCLYNCKDIVLRRNTAGSLGFCIVGGYEEYNGNKPFFIKSIV 672
               SCOP domains d3b76b                           _ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains 3b76B0                           0 B:401-502  [code=2.30.42.10, no name defined]                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....e---------------------------eeeeeeeee........eeee..eee..eee..eeeee...hhhhhhh......eeeee..ee.hhhhhhhhhhhhhh...eeeeeeeeeee----------------------------------------------------.----------------------eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PDZ  PDB: B:411-497 UniProt: 507-593                                                   --------------------------------------------PDZ  PDB: B:499-502                 PROSITE
           Transcript 1 (1) Exon 1.16  PDB: B:401-406 Exon 1.17  PDB: B:407-459 UniProt: 496-555 [INCOMPLETE]     ---------------------------------------------------------------------------Exon 1.19  PDB: B:499-502 (gaps)           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.18  PDB: B:459-498 UniProt: 555-631 [INCOMPLETE]                      ----------------------------------------- Transcript 1 (2)
                 3b76 B 401 NLYFQS---------------------------MHEKVVNIQKDPGESLGMTVAGGASHREWDLPIYVISVEPGGVISRDGRIKTGDILLNVDGVELTEVSRSEAVALLKRTSSSIVLKALEVKE----------------------------------------------------G----------------------SIV 502
                                 |   -         -         -   |   413       423       433       443       453       463       473       483       493    |    -         -         -         -         -       | -         -         -|  
                               406                         407                                                                                        498                                                  499                    500

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LNX1_HUMAN | Q8TBB1)

molecular function
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	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: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:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	3b76
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