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(-) Description

Title :  STRUCTURE OF LANGERIN CRD I313 D288 COMPLEXED WITH GLCNAC-BETA1-3GAL-BETA1-4GLCNAC-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) - 27 Nov 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GAL4Ligand/IonBETA-D-GALACTOSE
3MG1Ligand/IonMAGNESIUM ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL2Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 6 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GAL2Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
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 403
2AC2SOFTWAREGLU B:285 , ASN B:287 , GLU B:293 , ASN B:307 , ASP B:308 , NAG B:401BINDING SITE FOR RESIDUE CA B 403
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 403
5AC5SOFTWAREASN D:291 , HOH D:501 , HOH D:502BINDING SITE FOR RESIDUE MG D 404
6AC6SOFTWAREGLU A:285 , ASN A:287 , GLU A:293 , LYS A:299 , ASN A:307 , ASP A:308 , PRO A:310 , CA A:403 , HOH A:541 , HOH A:559 , HOH A:560 , HOH A:589 , SER C:237 , GLU C:240 , PHE C:241BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 401 TO 402
7AC7SOFTWAREGLU A:240 , PHE A:241 , GLU B:285 , ASN B:287 , GLU B:293 , LYS B:299 , ASN B:307 , ASP B:308 , CA B:403 , HOH B:520 , HOH B:527 , HOH B:591 , HOH B:592BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 401 TO 402
8AC8SOFTWAREGLU C:285 , ASN C:287 , GLU C:293 , LYS C:299 , ASN C:307 , ASP C:308 , CA C:403 , HOH C:547 , HOH C:570 , LYS D:203BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 401 TO 402
9AC9SOFTWAREPHE B:241 , HOH B:600 , GLU D:285 , ASN D:287 , GLU D:293 , LYS D:299 , ASN D:307 , ASP D:308 , CA D:403 , HOH D:579 , HOH D:600BINDING SITE FOR DI-SACCHARIDE NAG D 401 AND GAL D 402

(-) 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 4N38)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N38)

(-) Exons   (0, 0)

(no "Exon" information available for 4N38)

(-) 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 d4n38a_ 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
                 4n38 A 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNDAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317        


Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains d4n38b_ 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
                 4n38 B 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNDAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317        


Chain C from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains d4n38c_ 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
                 4n38 C 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNDAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYVP 325
                                   205       215       225       235       245       255       265       275       285       295       305       315       325


Chain D from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains d4n38d_ D: 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
                 4n38 D 197 QGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNDAGNNEHCGNIKAPSLQAWNDAPCDITFLFICKRPYV 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 4N38)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N38)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 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 4n35 4n36 4n37

(-) Related Entries Specified in the PDB File

4n32 4n33 4n34 4n35 4n36 4n37