Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DLN1 COMPLEXED WITH SUCROSE
 
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 :  1.86
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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3SUC2Ligand/IonSUCROSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , GLY A:15 , ARG A:87 , GLY A:131 , SER A:132 , ASP A:133 , ASP A:135 , HOH A:516 , HOH A:607 , HOH A:716 , HOH A:720binding site for residue SUC A 401
2AC2SOFTWAREGLY A:81 , GLY A:83 , GLY A:85 , HOH A:700binding site for residue CL A 402
3AC3SOFTWAREGLY B:14 , GLY B:15 , ARG B:87 , GLY B:131 , SER B:132 , ASP B:133 , ASP B:135 , HOH B:512 , HOH B:591 , HOH B:638binding site for residue SUC B 401
4AC4SOFTWAREGLY B:81 , ASN B:82 , GLY B:83 , GLY B:85 , HOH B:542binding site for residue CL B 402
5AC5SOFTWARESER A:107 , TRP A:108 , GLY A:109 , TRP B:39 , ALA B:84 , THR B:86 , TRP B:108 , HOH B:633 , HOH B:699binding site for residue EPE B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZNO)

(-) 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 .......ee...ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeeee..eeeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zno 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 .......ee...ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee...eeee....eeee....eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zno 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)
  - → 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 4ZNO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SUC  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4zno)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4zno
    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
  NATTL_DANRE | Q5CZR5
    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
  NATTL_DANRE | Q5CZR5
    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
        NATTL_DANRE | Q5CZR5: 4znq 4znr 5di0

(-) Related Entries Specified in the PDB File

4znq 4znr