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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF A SEED LECTIN FROM VATAIREA MACROCARPA COMPLEXED WITH TN-ANTIGEN
 
Authors :  B. L. Sousa, J. C. Silva-Filho, P. Kumar, A. Lyskowski, G. A. Bezerra, P. Delatorre, B. A. M. Rocha, C. S. Nagano, K. Gruber, B. S. Cavada
Date :  18 Jul 14  (Deposition) - 31 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lectin, Legume, Dalbergieae, Tn-Antigen, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Sousa, J. C. Silva Filho, P. Kumar, R. I. Pereira, A. Yskowski, B. A. Rocha, P. Delatorre, G. A. Bezerra, C. S. Nagano, K. Gruber, B. S. Cavada
High-Resolution Structure Of A New Tn Antigen-Binding Lecti From Vatairea Macrocarpa And A Comparative Analysis Of Tn-Binding Legume Lectins.
Int. J. Biochem. Cell Biol. V. 59C 103 2014
PubMed-ID: 25499445  |  Reference-DOI: 10.1016/J.BIOCEL.2014.12.002

(-) Compounds

Molecule 1 - SEED LECTIN
    Chains: A
    Organ: SEED
    Organism Scientific: VATAIREA MACROCARPA
    Organism Taxid: 77050
    Synonym: VML

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CIT1Ligand/IonCITRIC ACID
3MN1Ligand/IonMANGANESE (II) ION
4SO44Ligand/IonSULFATE ION
5TNR1Ligand/IonO-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CIT4Ligand/IonCITRIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
4SO416Ligand/IonSULFATE ION
5TNR4Ligand/IonO-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:123 , ASP A:125 , ASP A:132 , HIS A:137 , HOH A:503 , HOH A:526binding site for residue MN A 301
2AC2SOFTWAREASP A:125 , PHE A:127 , ASN A:129 , ASP A:132 , HOH A:488 , HOH A:501binding site for residue CA A 302
3AC3SOFTWAREASP A:87 , GLY A:105 , PHE A:127 , ASN A:129 , GLY A:212 , LEU A:213 , SER A:214 , HIS A:217 , SO4 A:304 , HOH A:494 , HOH A:497 , HOH A:533 , HOH A:618binding site for residue TNR A 303
4AC4SOFTWAREASN A:129 , THR A:130 , TNR A:303 , HOH A:443 , HOH A:537 , HOH A:602 , HOH A:604binding site for residue SO4 A 304
5AC5SOFTWARELYS A:84 , HIS A:217 , CIT A:308 , HOH A:497 , HOH A:525 , HOH A:552 , HOH A:603binding site for residue SO4 A 305
6AC6SOFTWARELYS A:149 , ARG A:215 , HOH A:419 , HOH A:451 , HOH A:474binding site for residue SO4 A 306
7AC7SOFTWARELYS A:38 , TYR A:150 , ARG A:215 , HOH A:427 , HOH A:461 , HOH A:610binding site for residue SO4 A 307
8AC8SOFTWARESER A:83 , LYS A:84 , THR A:85 , THR A:126 , PHE A:127 , SER A:128 , SER A:134 , ALA A:135 , ARG A:136 , HIS A:217 , SO4 A:305 , HOH A:430 , HOH A:508 , HOH A:525 , HOH A:552 , HOH A:565 , HOH A:620binding site for residue CIT A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U36)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:86 -Asp A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U36)

(-) Exons   (0, 0)

(no "Exon" information available for 4U36)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.ee....ee.eeeeeeeee..........eeeeeeee........hhhhh........eeeeee...........eeeeee......eeee........eeeeeeeehhh.eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u36 A   1 SEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQ 233
                                    10        20        30        40        50        60        70        80        90       100       110 ||    124       134       144       154       164       174       184       194       204       214       224         
                                                                                                                                         112|                                                                                                                    
                                                                                                                                          117
   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 4U36)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U36)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U36)

(-) Gene Ontology  (2, 2)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TNR  [ 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
    Ala A:86 - Asp A:87   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4u36
    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
  LECS_VATMA | P81371
    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
  LECS_VATMA | P81371
    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
        LECS_VATMA | P81371: 4u2a 4wv8 4xtm 4xtp 4xxa

(-) Related Entries Specified in the PDB File

4u2a 4U2A CONTAINS THE SAME PROTEIN COMPLEXED WITH N-ACETYL-D- GALACTOSAMINE.