Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF EXTRACELLULAR DOMAIN OF HUMAN LECTIN-LIKE TRANSCRIPT 1 (LLT1), THE LIGAND FOR NATURAL KILLER RECEPTOR-P1A
 
Authors :  S. Kita, H. Matsubara, Y. Kasai, T. Tamaoki, Y. Okabe, H. Fukuhara, J. Kamishikiryo, T. Ose, K. Kuroki, K. Maenaka
Date :  05 Sep 14  (Deposition) - 24 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Receptor, Ectodomain, Immunology, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kita, H. Matsubara, Y. Kasai, T. Tamaoki, Y. Okabe, H. Fukuhara, J. Kamishikiryo, E. Krayukhina, S. Uchiyama, T. Ose, K. Kuroki, K. Maenaka
Crystal Structure Of Extracellular Domain Of Human Lectin-Like Transcript 1 (Llt1), The Ligand For Natural Killer Receptor-P1A
Eur. J. Immunol. V. 45 1605 2015
PubMed-ID: 25826155  |  Reference-DOI: 10.1002/EJI.201545509

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 2 MEMBER D
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET22
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 71-191
    Gene: CLEC2D, CLAX, 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

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION
3ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:104 , ASP A:109 , HOH A:703binding site for residue ZN A 501
02AC2SOFTWARETYR A:88 , SER A:90 , ASP A:91 , ASP A:92 , PHE A:102 , TRP A:182binding site for residue ACT A 502
03AC3SOFTWAREASP B:92 , SO4 B:503binding site for residue ZN B 501
04AC4SOFTWAREGLU B:179 , SO4 B:503 , ASP C:109 , HOH C:813binding site for residue ZN B 502
05AC5SOFTWAREGLU B:179 , ZN B:501 , ZN B:502 , ASP C:109 , HOH C:813binding site for residue SO4 B 503
06AC6SOFTWAREASP B:104 , ASP B:109binding site for residue ZN B 504
07AC7SOFTWAREASP A:130 , GLU C:179 , ACT C:204 , HOH C:808binding site for residue ZN C 201
08AC8SOFTWAREGLU A:179 , ASP C:130 , ACT C:205 , HOH C:805 , HOH C:807binding site for residue ZN C 202
09AC9SOFTWAREGLU A:138 , ASP C:107 , HOH C:812binding site for residue ZN C 203
10AD1SOFTWAREASP A:130 , TYR A:165 , ARG A:180 , GLU C:179 , ZN C:201binding site for residue ACT C 204
11AD2SOFTWAREGLU A:179 , ASP C:130 , TYR C:165 , ARG C:180 , ZN C:202binding site for residue ACT C 205

(-) SS Bonds  (9, 9)

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
7C:75 -C:86
8C:103 -C:184
9C:163 -C:176

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WCO)

(-) 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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeee.......ee...........ee....eeee....eeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4wco A  71 LQAACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQELNFLLRYKGPSDHWIGLSREQGQPWKWINGTEWTRQFPILGAGECAYLNDKGASSARCYTERKWICSKS 187
                                    80        90       100       110       120       130       140       150       160       170       180       


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeee.....ee........ee....eeee....eeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4wco B  71 LQAACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQELNFLLRYKGPSDHWIGLSREQPWKWINWTRQFPILGAGECAYLNDKGASSARCYTERKWICSKSD 188
                                    80        90       100       110       120       130       142    || 155       165       175       185   
                                                                                             138|   147|                                     
                                                                                              141    151                                     


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeee.......ee.................eeee....eeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4wco C  74 ACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQELNFLLRYKGPSDHWIGLSREQGQPWKWINGTEWTRQFPILGAGECAYLNDKGASSARCYTERKWICSKS 187
                                    83        93       103       113       123       133       143       153       163       173       183
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4wco)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4wco
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CLC2D_HUMAN | Q9UHP7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CLC2D_HUMAN | Q9UHP7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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