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 :  LECTIN UEA-II COMPLEXED WITH NAG
 
Authors :  R. Loris, H. De Greve, M. -H. Dao-Thi, J. Messens, A. Imberty, L. Wyns
Date :  15 Nov 99  (Deposition) - 23 Nov 99  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lectin, Carbohydrate Binding, N-Acetylglucosamine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Loris, H. De Greve, M. -H. Dao-Thi, J. Messens, A. Imberty, L. Wyns
Structural Basis Of Carbohydrate Recognition By Lectin Ii From Ulex Europaeus, A Protein With A Promiscuous Carbohydrate Binding Site
J. Mol. Biol. V. 301 987 2000
PubMed-ID: 10966800  |  Reference-DOI: 10.1006/JMBI.2000.4016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITIN BINDING LECTIN, UEA-II
    Chains: A, B, C, D
    Organ: SEED
    Organism Common: FURZE
    Organism Scientific: ULEX EUROPAEUS
    Organism Taxid: 3902

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MN4Ligand/IonMANGANESE (II) ION
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:100 , SER A:101 , SER A:112 , LYS B:203BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWAREVAL A:85 , ASP A:86 , SER A:104 , ALA A:105 , GLY A:106 , TYR A:130 , ASN A:136 , GLY A:219 , ASN A:220 , LYS B:179BINDING SITE FOR RESIDUE NAG A 501
03AC3SOFTWAREPRO B:100 , SER B:112 , SER B:114 , PRO B:137BINDING SITE FOR RESIDUE NAG B 401
04AC4SOFTWAREPRO C:100 , SER C:101 , SER C:112BINDING SITE FOR RESIDUE NAG C 401
05AC5SOFTWAREASP C:86 , SER C:104 , ALA C:105 , GLY C:106 , TYR C:130 , ASN C:136 , GLY C:219 , ASN C:220BINDING SITE FOR RESIDUE NAG C 501
06AC6SOFTWARESER D:101 , SER D:112BINDING SITE FOR RESIDUE NAG D 401
07AC7SOFTWAREVAL D:85 , ASP D:86 , SER D:104 , ALA D:105 , GLY D:106 , TYR D:130 , ASN D:136 , GLY D:219 , ASN D:220BINDING SITE FOR RESIDUE NAG D 501
08AC8SOFTWAREGLU A:126 , ASP A:128 , ASP A:139 , HIS A:144BINDING SITE FOR RESIDUE MN A 301
09AC9SOFTWAREASP A:128 , TYR A:130 , ASN A:136 , ASP A:139BINDING SITE FOR RESIDUE CA A 302
10BC1SOFTWAREGLU B:126 , ASP B:128 , ASP B:139 , HIS B:144BINDING SITE FOR RESIDUE MN B 303
11BC2SOFTWAREASP B:128 , TYR B:130 , ASN B:136 , ASP B:139BINDING SITE FOR RESIDUE CA B 304
12BC3SOFTWAREGLU C:126 , ASP C:128 , ASP C:139 , HIS C:144BINDING SITE FOR RESIDUE MN C 305
13BC4SOFTWAREASP C:128 , TYR C:130 , ASN C:136 , ASP C:139BINDING SITE FOR RESIDUE CA C 306
14BC5SOFTWAREGLU D:126 , ASP D:128 , ASP D:139 , HIS D:144BINDING SITE FOR RESIDUE MN D 307
15BC6SOFTWAREASP D:128 , TYR D:130 , ASN D:136 , ASP D:139BINDING SITE FOR RESIDUE CA D 308

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:184 -C:184
2B:184 -D:184

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Val A:85 -Asp A:86
2Val B:85 -Asp B:86
3Lys C:41 -Pro C:42
4Val C:85 -Asp C:86
5Val D:85 -Asp D:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QOO)

(-) 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:235
 aligned with Q9FVF8_ULEEU | Q9FVF8 from UniProtKB/TrEMBL  Length:258

    Alignment length:237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
         Q9FVF8_ULEEU     3 SDDLSFNFDKFVPNQKNIIFQGAASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSTTGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSASMFGLFNSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDETSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDILSWYFTSNLE 239
               SCOP domains d1qooa_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qooA00 A:3-239  [code=2.60.120.200, n  o name defined]                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee................--...eeeeeee...............eeeeeeeee..........eeeeeeee.........hhhhh..............eeeeee...............eeeeee......eeee.......eeeeeeeeehhh.eeeeeee......eeeeeee.hhhhhh...eeeeeeeee.hhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qoo A   3 SDDLSFNFDKFVPNQKNIIFQGDASVSTTGVLQVTKVS--TTTSIGRALYAAPIQIWDSITGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSAGMFGLFSSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDGTSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDVLSWYFTSNLE 239
                                    12        22        32       | -|       52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
                                                                40 43                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:237
 aligned with Q9FVF8_ULEEU | Q9FVF8 from UniProtKB/TrEMBL  Length:258

    Alignment length:237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
         Q9FVF8_ULEEU     3 SDDLSFNFDKFVPNQKNIIFQGAASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSTTGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSASMFGLFNSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDETSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDILSWYFTSNLE 239
               SCOP domains d1qoob_ B: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qooB00 B:3-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee.....................eeeeeee...............eeeeeeeee..........eeeeeeee.........hhhhh........hhhhh.eeeeee...............eeeeee......eeee.......eeeeeeeeehhh.eeeeeee......eeeeeee.hhhhhh...eeeeeeeee.hhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qoo B   3 SDDLSFNFDKFVPNQKNIIFQGDASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSITGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSAGMFGLFSSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDGTSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDVLSWYFTSNLE 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with Q9FVF8_ULEEU | Q9FVF8 from UniProtKB/TrEMBL  Length:258

    Alignment length:237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
         Q9FVF8_ULEEU     3 SDDLSFNFDKFVPNQKNIIFQGAASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSTTGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSASMFGLFNSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDETSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDILSWYFTSNLE 239
               SCOP domains d1qooc_ C: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qooC00 C:3-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee.....................eeeeeee...............eeeeeeeee..........eeeeeeee.........hhhhh..............eeeeee...............eeeeee......eeee.......eeeeeeeeehhh.eeeeeee......eeeeeee.hhhhhh...eeeeeeeee.hhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qoo C   3 SDDLSFNFDKFVPNQKNIIFQGDASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSITGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSAGMFGLFSSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDGTSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDVLSWYFTSNLE 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       


Chain D from PDB  Type:PROTEIN  Length:237
 aligned with Q9FVF8_ULEEU | Q9FVF8 from UniProtKB/TrEMBL  Length:258

    Alignment length:237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
         Q9FVF8_ULEEU     3 SDDLSFNFDKFVPNQKNIIFQGAASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSTTGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSASMFGLFNSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDETSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDILSWYFTSNLE 239
               SCOP domains d1qood_ D: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1qooD00 D:3-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) -Lectin_legB-1qooD01 D:4-235                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) -Lectin_legB-1qooD02 D:4-235                                                                                                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) -Lectin_legB-1qooD03 D:4-235                                                                                                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) -Lectin_legB-1qooD04 D:4-235                                                                                                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author ...eeeee.........eeeee.....................eeeeeee...............eeeeeeeee..........eeeeeeee.........hhhhh..............eeeeee...............eeeeee......eeee.......eeeeeeeeehhh.eeeeeee......eeeeeee.hhhhhh...eeeeeeeee.hhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qoo D   3 SDDLSFNFDKFVPNQKNIIFQGDASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSITGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIPSGSSAGMFGLFSSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDGTSNIITASVDLKAILPEWVSVGFSGGVGNAAEFETHDVLSWYFTSNLE 239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9FVF8_ULEEU | Q9FVF8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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 ]
    MN  [ 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 ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys C:41 - Pro C:42   [ RasMol ]  
    Val A:85 - Asp A:86   [ RasMol ]  
    Val B:85 - Asp B:86   [ RasMol ]  
    Val C:85 - Asp C:86   [ RasMol ]  
    Val D:85 - Asp D:86   [ 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
  1qoo
    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
  Q9FVF8_ULEEU | Q9FVF8
    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
  Q9FVF8_ULEEU | Q9FVF8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9FVF8_ULEEU | Q9FVF8: 1dzq 1qos 1qot

(-) Related Entries Specified in the PDB File

1qnw LECTIN II FROM ULEX EUROPAEUS
1qos LECTIN UEA-II COMPLEXED WITH CHITOBIOSE
1qot LECTIN UEA-II COMPLEXED WITH FUCOSYLLACTOSE AND FUCOSYLGALACTOSELECTIN