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
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF LANGERIN CRD I313 COMPLEXED WITH GLCNAC-BETA1-3GAL-BETA1-4GLC-BETA-CH2CH2N3
 
Authors :  H. Feinberg, T. J. W. Rowntree, S. L. W. Tan, K. Drickamer, W. I. Weis, M. E
Date :  06 Oct 13  (Deposition) - 20 Nov 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,C  (1x)
Biol. Unit 6:  B,D  (1x)
Keywords :  Crd Carbohydrate Complex, Carbohydrate-Recognition Domain, C-Type Lectin On Langerhans Cells, Carbohydrate/Sugar Binding, Receptor On Langerhans Cells, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Feinberg, T. J. Rowntree, S. L. Tan, K. Drickamer, W. I. Weis, M. E. Taylor
Common Polymorphisms In Human Langerin Change Specificity For Glycan Ligands.
J. Biol. Chem. V. 288 36762 2013
PubMed-ID: 24217250  |  Reference-DOI: 10.1074/JBC.M113.528000

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER K
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CARBOHYDRATE RECOGNITION DOMAIN
    Gene: CD207, CLEC4K
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LANGERIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A C 
Biological Unit 6 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2CA4Ligand/IonCALCIUM ION
3GAL4Ligand/IonBETA-D-GALACTOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1BGC-1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 5 (3, 5)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL2Ligand/IonBETA-D-GALACTOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 6 (3, 6)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL2Ligand/IonBETA-D-GALACTOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:285 , ASN A:287 , GLU A:293 , ASN A:307 , ASP A:308 , NAG A:401BINDING SITE FOR RESIDUE CA A 404
2AC2SOFTWAREGLU B:285 , ASN B:287 , GLU B:293 , ASN B:307 , ASP B:308 , NAG B:401BINDING SITE FOR RESIDUE CA B 404
3AC3SOFTWAREGLU C:285 , ASN C:287 , GLU C:293 , ASN C:307 , ASP C:308 , NAG C:401BINDING SITE FOR RESIDUE CA C 403
4AC4SOFTWAREGLU D:285 , ASN D:287 , GLU D:293 , ASN D:307 , ASP D:308 , NAG D:401BINDING SITE FOR RESIDUE CA D 404
5AC5SOFTWAREGLU A:285 , ASN A:287 , GLU A:293 , LYS A:299 , ASN A:307 , ASP A:308 , PRO A:310 , CA A:404 , HOH A:520 , HOH A:540 , HOH A:559 , HOH A:578 , HOH A:580 , HOH A:581 , HOH A:597 , HOH A:603 , HOH A:614 , HOH A:640 , SER C:237 , GLU C:240 , PHE C:241BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 401 TO 403
6AC6SOFTWARELYS A:203 , SER A:237 , GLU A:240 , PHE A:241 , HOH A:562 , GLU B:285 , ASN B:287 , GLU B:293 , LYS B:299 , ASN B:307 , ASP B:308 , CA B:404 , HOH B:514 , HOH B:532 , HOH B:535 , HOH B:548 , HOH B:584 , HOH B:609BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 401 TO 403
7AC7SOFTWAREGLU C:285 , ASN C:287 , GLU C:293 , LYS C:299 , ASN C:307 , ASP C:308 , CA C:403 , HOH C:566 , HOH C:569 , HOH C:581 , HOH C:582 , HOH C:627 , LYS D:203BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 401 TO 402
8AC8SOFTWARESER B:237 , GLU B:240 , PHE B:241 , HOH B:516 , HOH B:571 , GLU D:285 , ASN D:287 , GLU D:293 , LYS D:299 , ASN D:307 , ASP D:308 , CA D:404 , HOH D:526 , HOH D:543 , HOH D:546 , HOH D:550 , HOH D:554 , HOH D:567 , HOH D:569 , HOH D:605 , HOH D:635BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 401 TO 403

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:223 -A:319
2A:295 -A:311
3B:223 -B:319
4B:295 -B:311
5C:223 -C:319
6C:295 -C:311
7D:223 -D:319
8D:295 -D:311

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:285 -Pro A:286
2Glu B:285 -Pro B:286
3Glu C:285 -Pro C:286
4Glu D:285 -Pro D:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N35)

(-) Exons   (0, 0)

(no "Exon" information available for 4N35)

(-) 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:128
                                                                                                                                                                
               SCOP domains d4n35a_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n35 A 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317        


Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains d4n35b_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n35 B 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317        


Chain C from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains d4n35c_ C: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n35 C 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   205       215       225       235       245       255       265       275       285       295       305       315       325


Chain D from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains d4n35d_ D: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n35 D 197 QGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYV 324
                                   206       216       226       236       246       256       266       276       286       296       306       316
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N35)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N35)

(-) Gene Ontology  (11, 11)

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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
 
  Cis Peptide Bonds
    Glu A:285 - Pro A:286   [ RasMol ]  
    Glu B:285 - Pro B:286   [ RasMol ]  
    Glu C:285 - Pro C:286   [ RasMol ]  
    Glu D:285 - Pro D:286   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ 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 | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 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
  4n35
    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
  CLC4K_HUMAN | Q9UJ71
    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
  CLC4K_HUMAN | Q9UJ71
    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
        CLC4K_HUMAN | Q9UJ71: 3c22 3kqg 3p5d 3p5e 3p5f 3p5g 3p5h 3p5i 3p7f 3p7g 3p7h 4ak8 4n32 4n33 4n34 4n36 4n37 4n38

(-) Related Entries Specified in the PDB File

4n32 4n33 4n34 4n36 4n37 4n38