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(-) Description

Title :  CRYSTAL STRUCTURE OF DLN1 COMPLEXED WITH MAN(ALPHA1-2)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 :  1.90
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  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MAN4Ligand/IonALPHA-D-MANNOSE
5PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
6PG41Ligand/IonTETRAETHYLENE GLYCOL
7PGE5Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:81 , GLY A:83 , GLY A:85 , HOH A:676 , HOH A:758binding site for residue CL A 403
02AC2SOFTWAREHIS A:104 , MET A:105 , THR A:106 , SER A:107 , TRP A:108 , HOH A:547 , HOH A:756binding site for residue PEG A 404
03AC3SOFTWAREPRO A:70 , GLY A:71 , ASN A:96 , LYS A:97binding site for residue PGE A 405
04AC4SOFTWAREGLY A:38 , TRP A:39 , SER A:107 , HOH A:577 , TRP B:108 , GLY B:109 , LYS B:111binding site for residue PGE A 406
05AC5SOFTWAREGLU A:30 , LYS A:31 , TRP A:47 , HOH A:611binding site for residue PGE A 407
06AC6SOFTWARELYS A:92 , LYS A:94 , GLU A:100 , PHE A:102 , GLU A:113 , HOH A:614binding site for residue PG4 A 408
07AC7SOFTWAREGLY B:81 , ASN B:82 , GLY B:83 , GLY B:85binding site for residue CL B 403
08AC8SOFTWARESER A:107 , TRP A:108 , GLY A:109 , TRP B:39 , ALA B:84 , THR B:86 , TRP B:108 , HOH B:511binding site for residue EPE B 404
09AC9SOFTWAREGLU A:168 , ASN B:96 , LYS B:97 , HOH B:508binding site for residue PEG B 405
10AD1SOFTWAREHIS B:104 , MET B:105 , THR B:106 , TRP B:108 , HOH B:663 , HOH B:692 , HOH B:700binding site for residue PEG B 406
11AD2SOFTWAREHOH A:698 , LYS B:111 , THR B:112 , HOH B:661 , HOH B:762binding site for residue EDO B 407
12AD3SOFTWAREGLU B:30 , LYS B:31 , TRP B:47 , HOH B:618 , HOH B:653binding site for residue PGE B 408
13AD4SOFTWARELYS B:92 , PHE B:102 , GLU B:113 , HOH B:636binding site for residue PGE B 409
14AD5SOFTWAREGLY A:14 , GLY A:15 , ARG A:87 , GLY A:131 , SER A:132 , ASP A:133 , ASP A:135 , HOH A:517 , HOH A:521 , HOH A:561binding site for Poly-Saccharide residues MAN A 401 through MAN A 402
15AD6SOFTWAREGLY B:14 , GLY B:15 , ARG B:87 , GLY B:131 , SER B:132 , ASP B:133 , ASP B:135 , HOH B:553 , HOH B:617 , HOH B:626binding site for Poly-Saccharide residues MAN B 401 through MAN B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZNQ)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               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..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeee....eeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4znq A  -1 SHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeeee..eeeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4znq B  -1 SHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
   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 4ZNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        NATTL_DANRE | Q5CZR5: 4zno 4znr 5di0

(-) Related Entries Specified in the PDB File

4zno THE SAME PROTEIN COMPLEXED WITH SUCROSE
4znr