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 :  CARP FISHELECTIN, APO FORM
 
Authors :  S. Capaldi, B. Faggion, M. E. Carrizo, L. Destefanis, M. C. Gonzalez, M. M. Bovi, M. Galliano, H. L. Monaco
Date :  21 Nov 14  (Deposition) - 08 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Six-Blade Beta Propeller, Lectin, Eggs, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Capaldi, B. Faggion, M. E. Carrizo, L. Destefanis, M. C. Gonzalez, M. Perduca, M. Bovi, M. Galliano, H. L. Monaco
Three-Dimensional Structure And Ligand-Binding Site Of Carp Fishelectin (Fel).
Acta Crystallogr. , Sect. D V. 71 1123 2015
PubMed-ID: 25945578  |  Reference-DOI: 10.1107/S1399004715004174

(-) Compounds

Molecule 1 - FISH-EGG LECTIN
    Chains: A, B
    Organism Common: CARP,FANCY CARP,KOI,MIRROR CARP
    Organism Scientific: CYPRINUS CARPIO
    Organism Taxid: 7962
    Other Details: EGGS
    Synonym: FEL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL3Ligand/IonGLYCEROL
3IPA5Ligand/IonISOPROPYL ALCOHOL
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:26 , ASN A:27 , LYS A:45 , THR A:59 , TRP A:202 , ILE A:203 , NAG A:302 , IPA A:304 , HOH A:443 , HOH A:510BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARETHR A:59 , ILE A:203 , NAG A:301 , HOH A:510BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWAREASP A:14 , ASP A:82 , GLU A:170 , HOH A:401 , HOH A:402 , HOH A:403BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREGLY A:164 , LEU A:165 , TYR A:187 , NAG A:301 , HOH A:452 , HOH A:573BINDING SITE FOR RESIDUE IPA A 304
05AC5SOFTWAREGLY A:121 , LYS A:122 , PHE A:159 , HOH A:458BINDING SITE FOR RESIDUE IPA A 305
06AC6SOFTWAREGLY A:42 , SER A:43 , ASN A:58 , PHE A:64 , HOH A:489BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWARELYS B:11 , LEU B:26 , ASN B:27 , THR B:59 , NAG B:302 , HOH B:487 , HOH B:538BINDING SITE FOR RESIDUE NAG B 301
08AC8SOFTWARETHR B:59 , NAG B:301BINDING SITE FOR RESIDUE NAG B 302
09AC9SOFTWAREASP B:14 , ASP B:82 , GLU B:170 , HOH B:401 , HOH B:402 , HOH B:403BINDING SITE FOR RESIDUE CA B 303
10BC1SOFTWAREGLY B:8 , ASN B:9 , PHE B:30 , HOH B:427 , HOH B:604BINDING SITE FOR RESIDUE IPA B 304
11BC2SOFTWAREGLY B:164 , LEU B:165 , TYR B:187 , TRP B:202 , HOH B:447BINDING SITE FOR RESIDUE IPA B 305
12BC3SOFTWARELEU B:1 , MET B:205 , THR B:237BINDING SITE FOR RESIDUE IPA B 306
13BC4SOFTWAREGLY B:42 , SER B:43 , ASN B:58 , PHE B:64 , PHE B:71 , HOH B:582BINDING SITE FOR RESIDUE GOL B 307
14BC5SOFTWAREASN B:113 , GLY B:121 , LYS B:122 , ASN B:137 , PHE B:143 , HOH B:608BINDING SITE FOR RESIDUE GOL B 308

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:234
2A:100 -A:153
3A:128 -A:133
4A:208 -A:226
5B:3 -B:234
6B:100 -B:153
7B:128 -B:133
8B:208 -B:226

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:109 -Pro A:110
2Trp B:109 -Pro B:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RUQ)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eeeee..eeeee....eeeeee..eeeeeeee..eeeee..eeeee....eeeeee..eeeeeeee..eee......eeee.....eeeehhhhhh.........eee.....eeee....eeee....eeeee..............eeeeee..eeee.....eeee.....eeeee..........eeeee......eeeeeee..eeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ruq A   1 LDCTVIDGNLKQIDAGSGSVVGVNNLNETFVLIDNVFTKISGSLKHFSVGPAGQLGVNTANNIFKYQSGGFVQLAGLLKQVDAGGDQIIAGVNMYDDIYCLNMDANNKWPSSNTPWVQLNGKLKYYSCGPYSCWGVNSNDQIFIMKDVSSNVCSGSGSFINIPGLLSMIEVATDGSVFGVNSQGNLYQRTGVTRSKPDGTDWISMVACPNGHKHVSFDLGVLWLVCVDGSIRKCIL 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee..eeeee....eeeeee..eeeeeeee..eeeee..eeeee....eeeeee..eeeeeeee..eee......eeee.....eeeehhhhhh.........eee.....eeee...eeeee....eeeeee.............eeeeee..eeee.....eeee.....eeeee..........eeeee......eeeeeee..eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ruq B   1 LDCTVIDGNLKQIDAGSGSVVGVNNLNETFVLIDNVFTKISGSLKHFSVGPAGQLGVNTANNIFKYQSGGFVQLAGLLKQVDAGGDQIIAGVNMYDDIYCLNMDANNKWPSSNTPWVQLNGKLKYYSCGPYSCWGVNSNDQIFIMKDVSSNVCSGSGSFINIPGLLSMIEVATDGSVFGVNSQGNLYQRTGVTRSKPDGTDWISMVACPNGHKHVSFDLGVLWLVCVDGSIRKCILT 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 4RUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:109 - Pro A:110   [ RasMol ]  
    Trp B:109 - Pro B:110   [ RasMol ]  
 

(-) 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
  4ruq
    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
  FEL_CYPCA | P68512
    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
  FEL_CYPCA | P68512
    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
        FEL_CYPCA | P68512: 4rus

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RUQ)