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(-) Description

Title :  CRYSTAL STRUCTURE OF GALECTIN 8 WITH NDP52 PEPTIDE
 
Authors :  B. -W. Kim, S. B. Hong, J. H. Kim, D. H. Kwon, H. K. Song
Date :  27 Sep 12  (Deposition) - 20 Mar 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Autophagy, Innate Immunity, Carbohydrate Recognition Domain (Crd), Autophagy Adapter Molecule, Nad Binding, Ndp52 Peoptide Binding, Cytosol, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Kim, S. B. Hong, J. H. Kim, D. H. Kwon, H. K. Song
Structural Basis For Recognition Of Autophagic Receptor Ndp52 By The Sugar Receptor Galectin-8.
Nat Commun V. 4 1613 2013
PubMed-ID: 23511477  |  Reference-DOI: 10.1038/NCOMMS2606

(-) Compounds

Molecule 1 - GALECTIN-8
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-155. 184-317
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 372-385
    Gene: CALCOCO2, NDP52
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:45 , GLN A:47 , ARG A:59 , HIS A:65 , ARG A:69 , ASN A:79 , TRP A:86 , GLU A:89 , TYR A:93 , PEG A:402 , HOH A:615 , HOH A:668 , HOH A:680 , HOH A:685BINDING SITE FOR RESIDUE NAD A 401
2AC2SOFTWAREARG A:59 , NAD A:401 , HOH A:641BINDING SITE FOR RESIDUE PEG A 402
3AC3SOFTWARELYS A:279 , TYR C:380BINDING SITE FOR RESIDUE PEG A 403
4AC4SOFTWAREARG B:45 , GLN B:47 , ARG B:59 , HIS B:65 , ARG B:69 , ASN B:79 , TRP B:86 , GLU B:89 , TYR B:93 , PEG B:402 , HOH B:556BINDING SITE FOR RESIDUE NAD B 401
5AC5SOFTWARETYR B:141 , NAD B:401 , HOH B:573BINDING SITE FOR RESIDUE PEG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HAN)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ile A:17 -Pro A:18
2Lys A:57 -Pro A:58
3Leu A:185 -Pro A:186
4Ile B:17 -Pro B:18
5Lys B:57 -Pro B:58
6Leu B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HAN)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4hana1 A:-1-154 automated matches                                                                                                                          d4hana2 A:155-317 automated matches                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee.....eeee.........eeeeeee.......eeeeee..........eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeeeeee.....eeee.........eeeeeeee......eeeeeee....eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4han A  -1 GSMMLSLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSHMRLPFAARLNTPMGPGRTVVVKGEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPGMYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSW 317
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       184       194       204       214       224       234       244       254       264       274       284       294       304       314   
                                                                                                                                                                                        157|                                                                                                                                     
                                                                                                                                                                                         184                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4hanb1 B:-1-154 automated matches                                                                                                                          d4hanb2 B:155-317 automated matches                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee.....eeee........eeeeeeee.......eeeeee..........eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeeeeee.....eeee.........eeeeeeee......eeeeeee....eeeeeeeeehhhheeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4han B  -1 GSMMLSLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSHMRLPFAARLNTPMGPGRTVVVKGEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPGMYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSW 317
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       184       194       204       214       224       234       244       254       264       274       284       294       304       314   
                                                                                                                                                                                        157|                                                                                                                                     
                                                                                                                                                                                         184                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4han C 372 PGLAYGNPY 380


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4han D 372 PGLAYGNPY 380
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CACO2_HUMAN | Q13137: 2mxp 3vvv 3vvw 4gxl 4xkl 5aaq
        LEG8_HUMAN | O00214: 2yro 2yv8 2yxs 3ap4 3ap5 3ap6 3ap7 3ap9 3apb 3ojb 3vkl 3vkm 3vkn 3vko 4bmb 4bme 4fqz 4gxl 5gzc 5gzd 5gze 5gzf 5gzg 5t7i 5t7s 5t7t 5t7u

(-) Related Entries Specified in the PDB File

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