Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF LECTIN FROM THE SEA MUSSEL CRENOMYTILUS GRAYANUS
 
Authors :  J. Lubkowski, M. Jakob, B. O'Keefe, A. Wlodawer
Date :  21 Sep 15  (Deposition) - 11 Nov 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Lectin, Sea Vertebrate, Recombinant, Trefoil, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jakob, J. Lubkowski, B. R. O'Keefe, A. Wlodawer
Structure Of A Lectin From The Sea Mussel Crenomytilus Grayanus (Cgl).
Acta Crystallogr. , Sect. F V. 71 1429 2015
PubMed-ID: 26527272  |  Reference-DOI: 10.1107/S2053230X15019858

(-) Compounds

Molecule 1 - GALNAC/GAL-SPECIFIC LECTIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CRENOMYTILUS GRAYANUS
    Organism Taxid: 151218
    Other Details: THE SYNTHETIC GENE WAS CLONED IN THE GATEWAY (R) SYSTEM WITH THE N-TERMINAL HIS6-TAG
    Other Details - Source: NON-OPTIMIZED SEQUENCE SYNTHESIZED BY BIOIBASIC

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric Unit (1, 18)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 5 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:16 , PRO A:17 , TYR A:18 , GLY A:19 , GLY A:20 , VAL A:31 , HIS A:33 , ASP A:35 , HIS A:37 , ASN A:119binding site for residue GOL A 201
02AC2SOFTWAREASN A:27 , HIS A:64 , GLY A:67 , GLY A:68 , HIS A:81 , ASP A:83 , HIS A:85binding site for residue GOL A 202
03AC3SOFTWAREGLU A:75 , HIS A:108 , PRO A:109 , LYS A:110 , GLY A:111 , GLY A:112 , VAL A:123 , HIS A:125 , HIS A:129 , HOH A:330binding site for residue GOL A 203
04AC4SOFTWAREHIS B:16 , GLY B:19 , GLY B:20 , HIS B:33 , ASP B:35 , HIS B:37 , ASN B:119binding site for residue GOL B 201
05AC5SOFTWAREASN B:27 , HIS B:64 , GLY B:67 , GLY B:68 , HIS B:81 , ASP B:83 , HIS B:85 , HOH B:334binding site for residue GOL B 202
06AC6SOFTWAREGLU B:75 , HIS B:108 , PRO B:109 , LYS B:110 , GLY B:111 , GLY B:112 , VAL B:123 , HIS B:125 , HIS B:129 , HOH B:333binding site for residue GOL B 203
07AC7SOFTWAREHIS C:16 , GLY C:19 , GLY C:20 , HIS C:33 , ASP C:35 , HIS C:37 , ASN C:119binding site for residue GOL C 201
08AC8SOFTWAREHOH B:304 , HOH B:320 , ASN C:27 , HIS C:64 , TYR C:66 , GLY C:67 , GLY C:68 , HIS C:81 , HIS C:85 , HOH C:302binding site for residue GOL C 202
09AC9SOFTWAREGLU C:75 , HIS C:108 , PRO C:109 , LYS C:110 , GLY C:111 , GLY C:112 , VAL C:123 , HIS C:125 , HIS C:129binding site for residue GOL C 203
10AD1SOFTWARETYR A:18 , HOH A:302 , HIS D:16 , PRO D:17 , GLY D:19 , GLY D:20 , HIS D:33 , ASP D:35 , HIS D:37 , ASN D:119binding site for residue GOL D 201
11AD2SOFTWAREASN D:27 , HIS D:64 , GLY D:67 , GLY D:68 , ASP D:83 , HIS D:85binding site for residue GOL D 202
12AD3SOFTWAREGLU D:75 , HIS D:108 , PRO D:109 , LYS D:110 , GLY D:111 , GLY D:112 , HIS D:125 , HIS D:129 , HOH D:332binding site for residue GOL D 203
13AD4SOFTWAREHIS E:16 , PRO E:17 , GLY E:19 , GLY E:20 , ASP E:35 , HIS E:37 , ASN E:119binding site for residue GOL E 201
14AD5SOFTWAREHOH A:304 , ASN E:27 , HIS E:64 , GLY E:67 , GLY E:68 , HIS E:81 , HIS E:85binding site for residue GOL E 202
15AD6SOFTWAREGLU E:75 , HIS E:108 , LYS E:110 , GLY E:111 , GLY E:112 , HIS E:125 , HIS E:129binding site for residue GOL E 203
16AD7SOFTWAREHIS F:16 , PRO F:17 , GLY F:19 , GLY F:20 , HIS F:33 , ASP F:35 , HIS F:37 , ASN F:119binding site for residue GOL F 201
17AD8SOFTWAREHOH E:302 , HOH E:353 , ASN F:27 , HIS F:64 , TYR F:66 , GLY F:67 , GLY F:68 , HIS F:81 , ASP F:83 , HIS F:85binding site for residue GOL F 202
18AD9SOFTWAREGLU F:75 , HIS F:108 , PRO F:109 , LYS F:110 , GLY F:111 , GLY F:112 , HIS F:125 , HIS F:129binding site for residue GOL F 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DUY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DUY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DUY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DUY)

(-) Exons   (0, 0)

(no "Exon" information available for 5DUY)

(-) Sequences/Alignments

Asymmetric 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeee..........eeeeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duy A   1 MTTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeee............eeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duy B   1 MTTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain C from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeee..........eeeeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duy C   1 MTTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeee............eeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5duy D   2 TTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         


Chain E from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeee............eeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duy E   1 MTTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain F from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeee............eeee...hhhh.eeeeeee..eeeeee.....eeee............eeee...hhhh.eeee....eeee....eeee..........eeeeee...hhhh.eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duy F   1 MTTFLIKHKASGKFLHPYGGSSNPANNTKLVLHSDIHERMYFQFDVVDERWGYIKHVASGKIVHPYGGQANPPNETNMVLHQDRHDRALFAMDFFNDNIMHKGGKYIHPKGGSPNPPNNTETVIHGDKHAAMEFIFVSPKNKDKRVLVYA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 5DUY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DUY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DUY)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    GOL  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5duy)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 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
  5duy
    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
  H2FH31_9BIVA | H2FH31
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  H2FH31_9BIVA | H2FH31
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        H2FH31_9BIVA | H2FH31: 5f8s 5f8w 5f8y 5f90

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DUY)