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 :  STRUCTURE OF A MANNOSE-SPECIFIC JACALIN-RELATED LECTIN FROM MORUS NIGRA
 
Authors :  A. Rabijns, A. Barre, E. J. M. Van Damme, W. J. Peumans, C. J. De Ranter,
Date :  08 Nov 04  (Deposition) - 25 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetrameric B-Prism Fold, Jacalin-Fold, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rabijns, A. Barre, E. J. M. Van Damme, W. J. Peumans, C. J. De Ranter P. Rouge
Structural Analysis Of The Jacalin-Related Lectin Mornigam From The Black Mulberry (Morus Nigra) In Complex With Mannose
Febs J. V. 272 3725 2005
PubMed-ID: 16008570  |  Reference-DOI: 10.1111/J.1742-4658.2005.04801.X

(-) Compounds

Molecule 1 - MANNOSE-BINDING LECTIN
    Chains: A, B, C, D
    Organism Scientific: MORUS NIGRA
    Organism Taxid: 85232
    Synonym: MANNOSE-SPECIFIC JACALIN-RELATED LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2GOL4Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:27 , ASN B:28 , ALA B:29 , ARG B:147 , HOH B:3078 , HOH B:3095 , HOH C:1502BINDING SITE FOR RESIDUE SO4 B 3018
2AC2SOFTWAREALA C:29 , ARG C:147BINDING SITE FOR RESIDUE ACY C 1424
3AC3SOFTWARELYS A:79 , ASN D:28 , ALA D:29 , ARG D:147BINDING SITE FOR RESIDUE ACY D 1425
4AC4SOFTWAREALA A:29 , ARG A:147BINDING SITE FOR RESIDUE ACY A 1426
5AC5SOFTWAREGLY B:27 , GLY B:149 , PHE B:150 , VAL B:151 , ASP B:153 , HOH B:3091 , PHE C:75 , THR C:77 , HOH C:1589BINDING SITE FOR RESIDUE GOL B 1370
6AC6SOFTWAREGLY A:26 , GLY A:27 , GLY A:149 , PHE A:150 , VAL A:151 , ASP A:153 , HOH C:1506BINDING SITE FOR RESIDUE GOL A 1371
7AC7SOFTWAREGLY C:27 , GLY C:149 , PHE C:150 , VAL C:151 , ASP C:153 , HOH C:1479 , HOH C:1588BINDING SITE FOR RESIDUE GOL C 1372
8AC8SOFTWAREGLY D:27 , GLY D:149 , PHE D:150 , VAL D:151 , ASP D:153 , HOH D:1506 , HOH D:1553 , HOH D:1564BINDING SITE FOR RESIDUE GOL D 1373

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XXQ)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:20 -Leu A:21
2Phe A:84 -Pro A:85
3Gly A:122 -Pro A:123
4Gly B:20 -Leu B:21
5Phe B:84 -Pro B:85
6Gly B:122 -Pro B:123
7Gly C:20 -Leu C:21
8Phe C:84 -Pro C:85
9Gly C:122 -Pro C:123
10Gly D:20 -Leu D:21
11Phe D:84 -Pro D:85
12Gly D:122 -Pro D:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XXQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XXQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1XXQ)

(-) 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:154
 aligned with Q8LGR3_MORNI | Q8LGR3 from UniProtKB/TrEMBL  Length:161

    Alignment length:154
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    
         Q8LGR3_MORNI     8 TQTTGTSQTVEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLPRLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGVHLSL 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xxqA00 A:8-161  [code=2.100.10.30, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee...........eeeeee.......eeeeeeeee..........eeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxq A   8 TQTTGTSQTIEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLARLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGFHLSL 161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q8LGR3_MORNI | Q8LGR3 from UniProtKB/TrEMBL  Length:161

    Alignment length:154
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    
         Q8LGR3_MORNI     8 TQTTGTSQTVEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLPRLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGVHLSL 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xxqB00 B:8-161  [code=2.100.10.30, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeee.hhhh...eeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxq B   8 TQTTGTSQTIEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLARLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGFHLSL 161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    


Chain C from PDB  Type:PROTEIN  Length:154
 aligned with Q8LGR3_MORNI | Q8LGR3 from UniProtKB/TrEMBL  Length:161

    Alignment length:154
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    
         Q8LGR3_MORNI     8 TQTTGTSQTVEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLPRLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGVHLSL 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xxqC00 C:8-161  [code=2.100.10.30, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeee.hhhh...eeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxq C   8 TQTTGTSQTIEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLARLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGFHLSL 161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    


Chain D from PDB  Type:PROTEIN  Length:154
 aligned with Q8LGR3_MORNI | Q8LGR3 from UniProtKB/TrEMBL  Length:161

    Alignment length:154
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    
         Q8LGR3_MORNI     8 TQTTGTSQTVEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLPRLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGVHLSL 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xxqD00 D:8-161  [code=2.100.10.30, no name defined]                                                                                                       CATH domains
           Pfam domains (1) -------------------Jacalin-1xxqD01 D:27-161                                                                                                                Pfam domains (1)
           Pfam domains (2) -------------------Jacalin-1xxqD02 D:27-161                                                                                                                Pfam domains (2)
           Pfam domains (3) -------------------Jacalin-1xxqD03 D:27-161                                                                                                                Pfam domains (3)
           Pfam domains (4) -------------------Jacalin-1xxqD04 D:27-161                                                                                                                Pfam domains (4)
         Sec.struct. author .........eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeee.hhhh...eeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxq D   8 TQTTGTSQTIEVGLWGGPGGNAWDDGSYTGIREINLSHGDAIGAFSVIYDLNGQPFTGPTHPGNEPSFKTVKITLDFPNEFLVSVSGYTGVLARLATGKDVIRSLTFKTNKKTYGPYGKEEGTPFSLPIENGLIVGFKGRSGFVVDAIGFHLSL 161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   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 1XXQ)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Jacalin] (35)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8LGR3_MORNI | Q8LGR3)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:122 - Pro A:123   [ RasMol ]  
    Gly A:20 - Leu A:21   [ RasMol ]  
    Gly B:122 - Pro B:123   [ RasMol ]  
    Gly B:20 - Leu B:21   [ RasMol ]  
    Gly C:122 - Pro C:123   [ RasMol ]  
    Gly C:20 - Leu C:21   [ RasMol ]  
    Gly D:122 - Pro D:123   [ RasMol ]  
    Gly D:20 - Leu D:21   [ RasMol ]  
    Phe A:84 - Pro A:85   [ RasMol ]  
    Phe B:84 - Pro B:85   [ RasMol ]  
    Phe C:84 - Pro C:85   [ RasMol ]  
    Phe D:84 - Pro D:85   [ 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
  1xxq
    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
  Q8LGR3_MORNI | Q8LGR3
    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
  Q8LGR3_MORNI | Q8LGR3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8LGR3_MORNI | Q8LGR3: 1xxr

(-) Related Entries Specified in the PDB File

1xxr THE SAME PROTEIN COMPLEXED WITH MANNOSE