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(-) Description

Title :  CRYSTAL STRUCTURE PTP DELTA IG1-FN2 IN COMPLEX WITH IL-1RACP
 
Authors :  A. Yamagata, S. Fukai
Date :  25 Feb 15  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trans-Synaptic Complex, Synapse Organizer, Immune System-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamagata, T. Yoshida, Y. Sato, S. Goto-Ito, T. Uemura, A. Maeda, T. Shiroshima, S. Iwasawa-Okamoto, H. Mori, M. Mishina, S. Fukai
Mechanisms Of Splicing-Dependent Trans-Synaptic Adhesion By Ptp Delta-Il1Rapl1/Il-1Racp For Synaptic Differentiation.
Nat Commun V. 6 6926 2015
PubMed-ID: 25908590  |  Reference-DOI: 10.1038/NCOMMS7926

(-) Compounds

Molecule 1 - INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: FREESTYLE 293-F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 21-351
    Gene: IL1RAP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IL-1RACP
 
Molecule 2 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: FREESTYLE 293-F
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 21-511
    Gene: PTPRD
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: R-PTP-DELTA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:261binding site for Mono-Saccharide NAG A 601 bound to ASN A 261
2AC2SOFTWARESER A:304 , ALA A:305 , ASN A:306 , GLN A:323binding site for Mono-Saccharide NAG A 602 bound to ASN A 306
3AC3SOFTWAREASN B:57 , SER B:59binding site for Mono-Saccharide NAG B 402 bound to ASN B 57
4AC4SOFTWAREASN B:107binding site for Mono-Saccharide NAG B 405 bound to ASN B 107
5AC5SOFTWARELEU B:29 , GLN B:75 , GLY B:110 , ASN B:111binding site for Mono-Saccharide NAG B 403 bound to ASN B 111
6AC6SOFTWAREASN B:118 , THR B:120binding site for Mono-Saccharide NAG B 401 bound to ASN B 118
7AC7SOFTWAREASN B:139 , PHE B:144 , ASN B:209binding site for Mono-Saccharide NAG B 404 bound to ASN B 209

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:52 -A:105
2A:154 -A:214
3A:264 -A:309
4B:24 -B:122
5B:47 -B:114
6B:137 -B:181
7B:160 -B:212
8B:266 -B:332

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Arg B:102 -Pro B:103
2Pro B:258 -Gly B:259
3Asp A:57 -Pro A:58
4Gln A:92 -Pro A:93
5Thr A:96 -Pro A:97
6Asn A:159 -Pro A:160
7Gly A:257 -Gly A:258
8Ser A:269 -Pro A:270

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YFD)

(-) 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:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeee....eeeeeeeeee...eeeeee..ee.....eeeee.....eeeeee.........eeeeeeeee..eeeeeeeeeeeehhhhh.....eeee....eeee....eeeeeeee.....eeeeee..ee.........eeeee........eeeeeee...hhhhheeeeeeeee..eeee...eeeeee.......eeeeeee....ee......eeeeeeeeee...eeeeee..ee..........eeeeee......eeeeeeeee..eeeeeeeeee...........eeeee...eeeee..........eeeeeeee.......eeeeee...eeeee......eeeeeeeee....eeee...eeee..........eeeeeee.....eeeeee..........eeeeeee.....hhhhheeeeee...eeee.......eeeeeeeee...........eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfd A  28 ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEESDQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVKALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSVAGLSPYSDYEFRVVAVNNIGRGPASEPVLTQTSEQAPSSAPRDVQARMLSSTTILVQWKEPEEPNGQIQGYRVYYTMDPTQHVNNWMKHNVADSQITTIGNLVPQKTYSVKVLAFTSIGDGPLSSDIQVIT 518
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517 


Chain B from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee....eeee.hhhh.....hhhhhhh...eeeeeeee......ee....hhhh.eeee..eeee...hhhh.eeeeeeee.....eeeeeeeeee.............eeeee.....eeee..............eeeeee..ee......eee...eeee........eeeeeeeeeee..eeeeeeeeeeeeee.........ee.....................eeee........eeeee............eeee..eee.....eeee.eeee...hhhhhhh..eeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfd B  24 CDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKYNYSTAHSSGLTLIWYWTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYCSKVAFPLEVVQKDSCFNSAMRFPVHKMYIEHGIHKITCPNVDGYFPSSVKPSVTWYKGCTEIVDFHNVLPEGMNLSFFIPLVSNNGNYTCVVTYPENGRLFHLTRTVTVKVVGSPKDALPPQIYSPNDRVVYEKEPGEELVIPCKVYFSFIMDSHNEVWWTIDGKKPDDVTVDITINESVSYSSTEDETRTQILSIKKVTPEDLRRNYVCHARNTKGEAEQAA 345
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   Legend:   → Mismatch (orange background)
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  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)

(no "SCOP Domain" information available for 4YFD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 41)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg B:102 - Pro B:103   [ RasMol ]  
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    Ser A:269 - Pro A:270   [ RasMol ]  
    Thr A:96 - Pro A:97   [ RasMol ]  
 

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  4yfd
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  IL1AP_MOUSE | Q61730
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  PTPRD_MOUSE | Q64487
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  3.1.3.48
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PTPRD_MOUSE | Q64487: 4y61 4yfc 4yfe 4yfg 4yh7

(-) Related Entries Specified in the PDB File

4yfc 4yfe 4yfg