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
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)

(-) Description

Title :  ARCELIN-5, A LECTIN-LIKE DEFENSE PROTEIN FROM PHASEOLUS VULGARIS
 
Authors :  T. Hamelryck, R. Loris
Date :  02 Oct 96  (Deposition) - 23 Dec 96  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Lectin-Like Proteins, Plant Defense Proteins, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hamelryck, F. Poortmans, A. Goossens, G. Angenon, M. Van Montagu, L. Wyns, R. Loris
Crystal Structure Of Arcelin-5, A Lectin-Like Defense Protein From Phaseolus Vulgaris
J. Biol. Chem. V. 271 32796 1996
PubMed-ID: 8955116  |  Reference-DOI: 10.1074/JBC.271.51.32796
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARCELIN-5A
    ChainsA, B
    OrganSEED
    Organism ScientificPHASEOLUS VULGARIS
    Organism Taxid3885
    StrainG02771
    SynonymARC5A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x) B
Biological Unit 2 (1x)A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:22 , ARG A:43 , ASP A:45 , LEU A:47 , LYS A:101 , NAG A:261 , FUC A:262BINDING SITE FOR RESIDUE NAG A 260
2AC2SOFTWAREASP A:45 , LYS A:101 , NAG A:260 , FUC A:262BINDING SITE FOR RESIDUE NAG A 261
3AC3SOFTWARELYS A:101 , NAG A:260 , NAG A:261BINDING SITE FOR RESIDUE FUC A 262
4AC4SOFTWAREASN B:22 , ARG B:43 , ASP B:45 , LEU B:47 , LYS B:101 , NAG B:261 , FUC B:262BINDING SITE FOR RESIDUE NAG B 260
5AC5SOFTWAREASP B:45 , LYS B:101 , NAG B:260 , FUC B:262BINDING SITE FOR RESIDUE NAG B 261
6AC6SOFTWARELYS B:101 , NAG B:260 , NAG B:261BINDING SITE FOR RESIDUE FUC B 262

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:146 -A:182
2B:146 -B:182

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:84 -Tyr A:85
2Ala B:84 -Tyr B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.AR5A_PHAVU215-224
 
  2A:194-203
B:194-203
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.AR5A_PHAVU215-224
 
  1-
B:194-203
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.AR5A_PHAVU215-224
 
  1A:194-203
-

(-) Exons   (0, 0)

(no "Exon" information available for 1IOA)

(-) 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:228
 aligned with AR5A_PHAVU | Q42460 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:228
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           AR5A_PHAVU    22 ATETSFNFPNFHTDDKLILQGNATISSKGQLQLTGVGSNELPRVDSLGRAFYSDPIQIKDSNNVASFNTNFTFIIRAKNQSISAYGLAFALVPVNSPPQKKQEFLGIFNTNNPEPNARTVAVVFNTFKNRIDFDKNFIKPYVNENCDFHKYNGEKTDVQITYDSSNNDLRVFLHFTVSQVKCSVSATVHLEKEVDEWVSVGFSATSGLTEDTTETHDVLSWSFSSKFR 249
               SCOP domains d1ioaa_ A: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                 SCOP domains
               CATH domains 1ioaA00 A:1-228  [code=2.60.120.200, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee........eeeee.........................eeeeee............eeeeeeeeee..........eeeeeeeee........hhh...............eeeeee....eeeeee......eeee..hhhh....eeeeeeee....eeeeeeee.....eeeeeee..hhh.....eeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ioa A   1 ATETSFNFPNFHTDDKLILQGNATISSKGQLQLTGVGSNELPRVDSLGRAFYSDPIQIKDSNNVASFNTNFTFIIRAKNQSISAYGLAFALVPVNSPPQKKQEFLGIFNTNNPEPNARTVAVVFNTFKNRIDFDKNFIKPYVNENCDFHKYNGEKTDVQITYDSSNNDLRVFLHFTVSQVKCSVSATVHLEKEVDEWVSVGFSPTSGLTEDTTETHDVLSWSFSSKFR 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with AR5A_PHAVU | Q42460 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:228
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           AR5A_PHAVU    22 ATETSFNFPNFHTDDKLILQGNATISSKGQLQLTGVGSNELPRVDSLGRAFYSDPIQIKDSNNVASFNTNFTFIIRAKNQSISAYGLAFALVPVNSPPQKKQEFLGIFNTNNPEPNARTVAVVFNTFKNRIDFDKNFIKPYVNENCDFHKYNGEKTDVQITYDSSNNDLRVFLHFTVSQVKCSVSATVHLEKEVDEWVSVGFSATSGLTEDTTETHDVLSWSFSSKFR 249
               SCOP domains d1ioab_ B: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                 SCOP domains
               CATH domains 1ioaB00 B:1-228  [code=2.60.120.200, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee........eeeee.........................eeeeee............eeeeeeeeee..........eeeeeeee.........hhh...............eeeeee....eeeeee......eeee..hhhh....eeeeeeee....eeeeeeee.....eeeeeee..hhh......eeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ioa B   1 ATETSFNFPNFHTDDKLILQGNATISSKGQLQLTGVGSNELPRVDSLGRAFYSDPIQIKDSNNVASFNTNFTFIIRAKNQSISAYGLAFALVPVNSPPQKKQEFLGIFNTNNPEPNARTVAVVFNTFKNRIDFDKNFIKPYVNENCDFHKYNGEKTDVQITYDSSNNDLRVFLHFTVSQVKCSVSATVHLEKEVDEWVSVGFSPTSGLTEDTTETHDVLSWSFSSKFR 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IOA)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AR5A_PHAVU | Q42460)
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.
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.

 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
    FUC  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:84 - Tyr A:85   [ RasMol ]  
    Ala B:84 - Tyr B:85   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ioa
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AR5A_PHAVU | Q42460
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AR5A_PHAVU | Q42460
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1IOA)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IOA)