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(-) Description

Title :  CRYSTAL STRUCTURE OF DLN1 COMPLEXED WITH MAN(ALPHA1-3)MAN
 
Authors :  N. Jia, Y. L. Jiang, W. Cheng, H. W. Wang, C. Z. Zhou, Y. Chen
Date :  05 May 15  (Deposition) - 20 Jan 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pore-Forming Protein, Aeolysin-Like Protein, Vetebrate, High-Mannose Glycans, Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Jia, N. Liu, W. Cheng, Y. L. Jiang, H. Sun, L. L. Chen, J. Peng, Y. Zhang Y. H. Ding, Z. H. Zhang, X. Wang, G. Cai, J. Wang, M. Q. Dong, Z. Zhang, H. Wu, H. W. Wang, Y. Chen, C. Z. Zhou
Structural Basis For Receptor Recognition And Pore Formatio Of A Zebrafish Aerolysin-Like Protein.
Embo Rep. V. 17 235 2016
PubMed-ID: 26711430  |  Reference-DOI: 10.15252/EMBR.201540851

(-) Compounds

Molecule 1 - NATTERIN-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 23)

Asymmetric/Biological Unit (8, 23)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CL2Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5MAN4Ligand/IonALPHA-D-MANNOSE
6PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
7PG43Ligand/IonTETRAETHYLENE GLYCOL
8PGE4Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:81 , GLY A:83 , GLY A:85binding site for residue CL A 403
02AC2SOFTWARETHR A:5 , ASN A:6 , LEU A:7 , HOH A:501 , HOH A:560binding site for residue PEG A 404
03AC3SOFTWAREASN A:25 , GLY A:26 , ASP A:50 , THR A:202 , TYR A:292 , HOH A:529binding site for residue PEG A 405
04AC4SOFTWAREHIS A:104 , MET A:105 , THR A:106 , TRP A:108 , HOH A:510 , HOH A:605 , EPE B:404binding site for residue PGE A 406
05AC5SOFTWARELYS A:97 , HOH A:520 , GLU B:168 , LYS B:191binding site for residue PGE A 407
06AC6SOFTWAREGLU A:30 , LYS A:31 , TRP A:47 , VAL A:67 , HOH A:622 , VAL B:67binding site for residue PG4 A 408
07AC7SOFTWARELYS A:92 , LYS A:94 , GLU A:100 , PHE A:102 , GLU A:113binding site for residue PG4 A 409
08AC8SOFTWARESER A:17binding site for residue EDO A 410
09AC9SOFTWAREGLY B:81 , ASN B:82 , GLY B:83 , GLY B:85binding site for residue CL B 403
10AD1SOFTWARESER A:107 , GLY A:109 , PGE A:406 , TRP B:39 , THR B:86 , TRP B:108 , HOH B:503binding site for residue EPE B 404
11AD2SOFTWARELYS B:307 , ASN B:309binding site for residue EDO B 405
12AD3SOFTWAREVAL B:127 , GLY B:128binding site for residue EDO B 406
13AD4SOFTWARETHR B:5 , ASN B:6 , LEU B:7 , HOH B:617binding site for residue PEG B 407
14AD5SOFTWAREGLY A:38 , TRP A:39 , SER A:107 , GLY B:109binding site for residue PEG B 408
15AD6SOFTWARESER B:147 , LYS B:182 , GLU B:212 , THR B:236 , HOH B:502binding site for residue PEG B 409
16AD7SOFTWAREGLU B:30 , LYS B:31 , TRP B:47 , HOH B:516binding site for residue PGE B 410
17AD8SOFTWAREHIS B:104 , MET B:105 , THR B:106 , SER B:107 , TRP B:108 , LEU B:110 , HOH B:519binding site for residue PGE B 411
18AD9SOFTWARELYS B:92 , LYS B:94 , GLU B:100 , PHE B:102 , GLU B:113binding site for residue PG4 B 412
19AE1SOFTWAREGLU A:168 , GLY B:71 , ASN B:96 , LYS B:97 , HOH B:501binding site for residue 1PE B 413
20AE2SOFTWAREGLY A:15 , ARG A:87 , GLY A:131 , SER A:132 , ASP A:133 , ASP A:135 , HOH A:502 , MAN B:401binding site for Poly-Saccharide residues MAN A 401 through MAN A 402
21AE3SOFTWAREMAN A:401 , GLY B:14 , GLY B:15 , ARG B:87 , GLY B:131 , SER B:132 , ASP B:133 , ASP B:135 , HOH B:654binding site for Poly-Saccharide residues MAN B 401 through MAN B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZNR)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee..ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..hhhhh...eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeee....eeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4znr A  -2 GSHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee..ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..hhhhh...eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeee....eeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4znr B  -2 GSHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   Legend:   → Mismatch (orange background)
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  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 4ZNR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        NATTL_DANRE | Q5CZR5: 4zno 4znq 5di0

(-) Related Entries Specified in the PDB File

4zno 4znq