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(-) Description

Title :  DIMERIC FORM OF HUMAN LLT1, A LIGAND FOR NKR-P1
 
Authors :  T. Skalova, J. Blaha, K. Harlos, J. Duskova, T. Koval, J. Stransky, J. Ha O. Vanek, J. Dohnalek
Date :  06 Jun 14  (Deposition) - 11 Mar 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  C-Type Lectin Like Fold, Ligand For Human Receptor Nkr-P1, Glycosylation; Deglycosylated After The First Glcnac Unit, Anchored In Membrane On Cell Surface, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Skalova, J. Blaha, K. Harlos, J. Duskova, T. Koval', J. Stransky, J. Hasek, O. Vanek, J. Dohnalek
Four Crystal Structures Of Human Llt1, A Ligand Of Human Nkr-P1, In Varied Glycosylation And Oligomerization States
Acta Crystallogr. , Sect. D V. 71 578 2015
PubMed-ID: 25760607  |  Reference-DOI: 10.1107/S1399004714027928

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 2 MEMBER D
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PTT28
    Expression System Strain: HEK293S GNTI-
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR PART, UNP RESIDUES 72-191
    Gene: CLAX, CLEC2B, CLEC2D, LLT1, OCIL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LECTIN-LIKE NK CELL RECEPTOR, LECTIN-LIKE TRANSCRIPT 1, LLT- 1, OSTEOCLAST INHIBITORY LECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:95 , THR A:97 , SER A:98 , ASP A:168 , HOH A:406 , HOH A:469 , SER B:105 , HOH B:453BINDING SITE FOR MONO-SACCHARIDE NAG A 301 BOUND TO ASN A 95
2AC2SOFTWAREGLN A:112 , GLU A:114 , TRP A:145 , ASN A:147 , HOH A:401 , HOH A:413 , HOH A:434 , ARG B:153 , GLN B:154 , ARG B:175 , THR B:178 , ARG B:180 , HOH B:415BINDING SITE FOR MONO-SACCHARIDE NAG A 302 BOUND TO ASN A 147
3AC3SOFTWAREGLY A:159 , THR A:193 , ASN B:95 , SER B:98 , PHE B:116 , LYS B:169 , HOH B:402 , HOH B:419 , HOH B:461 , HOH B:475 , HOH B:483BINDING SITE FOR MONO-SACCHARIDE NAG B 301 BOUND TO ASN B 95
4AC4SOFTWAREARG A:153 , GLN B:112 , GLU B:114 , TRP B:145 , ASN B:147 , THR B:149 , HOH B:441 , HOH B:481BINDING SITE FOR MONO-SACCHARIDE NAG B 302 BOUND TO ASN B 147

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:75 -A:86
2A:103 -A:184
3A:163 -A:176
4B:75 -B:86
5B:103 -B:184
6B:163 -B:176

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4QKI)

(-) Sequences/Alignments

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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhh...eeeeee..........................eeee....eeee......eeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qki A  73 AACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQELNFLLRYKGPSDHWIGLSREQGQPWKWINGTEWTRQFPILGAGECAYLNDKGASSARCYTERKWICSKSDIHVGTK 194
                                    82        92       102       112       122       132       142       152       162       172       182       192  


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeee.......ee.................eeee....eeee......eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qki B  73 AACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQELNFLLRYKGPSDHWIGLSREQGQPWKWINGTEWTRQFPILGAGECAYLNDKGASSARCYTERKWICSKSDIHVG 192
                                    82        92       102       112       122       132       142       152       162       172       182       192
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  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 4QKI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        CLC2D_HUMAN | Q9UHP7: 4qkg 4qkh 4qkj 4wco

(-) Related Entries Specified in the PDB File

4qkg 4qkh 4qkj