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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PTPDELTA AND HUMAN SLITRK1 COMPLEX
 
Authors :  H. M. Kim, B. S. Park, D. Kim, S. G. Lee
Date :  15 Sep 14  (Deposition) - 19 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Leucine Rich-Repeat, Ig-Like Domain, Synaptic Adhesion, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Um, K. H. Kim, B. S. Park, Y. Choi, D. Kim, C. Y. Kim, S. J. Kim, M. Kim, J. S. Ko, S. G. Lee, G. Choii, J. Nam, W. D. Heo, E. Kim, J. O. Lee, J. Ko, H. M. Kim
Structural Basis For Lar-Rptp/Slitrk Complex-Mediated Synaptic Adhesion.
Nat Commun V. 5 5423 2014
PubMed-ID: 25394468  |  Reference-DOI: 10.1038/NCOMMS6423

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: PTPRD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE DELTA, R-PTP-DELTA
 
Molecule 2 - SLIT AND NTRK-LIKE PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: SLITRK1, KIAA1910, LRRC12, UNQ233/PRO266
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUCINE-RICH REPEAT-CONTAINING PROTEIN 12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:299 , GLN A:316BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWAREASN A:254 , GLU A:290BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWAREARG B:238 , VAL B:239 , ASP B:251 , LEU B:252 , ASN B:253BINDING SITE FOR RESIDUE SO4 B 301
4AC4SOFTWAREASN B:253BINDING SITE FOR RESIDUE NAG B 302

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:98
2A:147 -A:207
3A:257 -A:302
4B:24 -B:31
5B:29 -B:42
6B:216 -B:241
7B:218 -B:261

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Asp A:50 -Pro A:51
2Gln A:85 -Pro A:86
3Thr A:89 -Pro A:90
4Glu A:93 -Ala A:94
5Asn A:152 -Pro A:153
6Ser A:262 -Pro A:263
7Val B:23 -Cys B:24
8Ile B:34 -Glu B:35
9Ala B:243 -Pro B:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RCA)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee....eeee....eeeeeeee.....eeeeee..ee.....eeeee.....eeeeee.........eeeeeeee....eeeeeeeeeee..........eeee....eeee....eee..eee.....eeeeee..ee.........eee..............eee........eeeeeeee....eee...eeeeee.......eeeeeee....eee...eeeeeeeeeeee...eeeeee..ee..hhhhh...eeeeeeeee...eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rca A  21 ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEESDQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK 320
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee...................eeee.......ee....hhhhh.eeeee.......ee............eee.......ee............eee.......ee.hhhh.......eee....................eee......................eee.....ee....hhhhhhhhhhh..........eee.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rca B  22 DVCKEKICSCNEIEGDLHVDCEKKGFTSLQRFTAPTSQFYHLFLHGNSLTRLFPNEFANFYNAVSLHMENNGLHEIVPGAFLGLQLVKRLHINNNKIKSFRKQTFLGLDDLEYLQADFNLLRDIDPGAFQDLNKLEVLILNDNLISTLPANVFQYVPITHLDLRGNRLKTLPYEEVLEQIPGIAEILLEDNPWDCTCDLLSLKEWLENIPKNALIGRVVCEAPTRLQGKDLNETTEQDLCP 262
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4RCA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 31)

Asymmetric/Biological Unit(hide GO term definitions)

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  4rca
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  PTPRD_HUMAN | P23468
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  SLIK1_HUMAN | Q96PX8
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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_HUMAN | P23468: 1x5z 2dlh 2yd6 2yd7
        SLIK1_HUMAN | Q96PX8: 4rcw

(-) Related Entries Specified in the PDB File

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