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

(-) Description

Title :  THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX
 
Authors :  S. N. Ruzeinikov, I. Y. Mikhailova, I. N. Tsygannik, W. Pangborn, W. Dua V. Z. Pletnev
Date :  17 Aug 98  (Deposition) - 26 Aug 98  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Pea Lectin, D-Mannopyranose Complex, Carbohydrate Binding, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Ruzheinikov, I. Y. Mikhailova, I. N. Tsygannik, W. Pangborn, W. Duax, V. Z. Pletnev
The Structure Of The Pea Lectin-D-Mannopyranose Complex At 2. 1 A Resolution
Russ. J. Bioorganic Chem. V. 24 277 1998
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN (LECTIN)
    Chains: A, C
    Fragment: BETA CHAIN
    Organ: SEEDS
    Organism Common: PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888
 
Molecule 2 - PROTEIN (LECTIN)
    Chains: B, D
    Fragment: ALPHA CHAIN
    Organ: SEEDS
    Organism Common: PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN1Ligand/IonALPHA-D-MANNOSE
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN1Ligand/IonALPHA-D-MANNOSE
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWAREGLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:302 , HOH A:306BINDING SITE FOR RESIDUE MN A 301
3AC3SOFTWAREALA A:80 , ASP A:81 , GLY A:99 , PHE A:123 , ASN A:125 , GLY B:216 , ALA B:217 , GLU B:218 , HOH B:404 , HOH B:405 , HOH B:421BINDING SITE FOR RESIDUE MAN B 401
4AC4SOFTWAREALA A:80 , ASP A:81 , GLY A:98 , GLY A:99 , PHE A:123 , ASN A:125 , GLY B:216 , ALA B:217 , GLU B:218 , HOH B:404 , HOH B:405 , HOH B:416BINDING SITE FOR RESIDUE BMA B 403
5AC5SOFTWAREALA C:80 , ASP C:81 , GLY C:98 , GLY C:99 , PHE C:123 , ASN C:125 , HOH C:424 , GLY D:216 , ALA D:217 , GLU D:218BINDING SITE FOR RESIDUE MAN C 402
6AC6SOFTWAREALA C:80 , ASP C:81 , GLY C:98 , GLY C:99 , PHE C:123 , ASN C:125 , HOH C:436 , GLY D:216 , ALA D:217 , GLU D:218BINDING SITE FOR RESIDUE BMA C 404
7AC7SOFTWAREASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:405 , HOH C:408BINDING SITE FOR RESIDUE CA C 302
8AC8SOFTWAREGLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:406 , HOH C:407BINDING SITE FOR RESIDUE MN C 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:80 -Asp A:81
2Ala C:80 -Asp C:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_PEA146-152
 		  2A:116-122
C:116-122
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_PEA233-242
 		  2B:203-212
D:203-212
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_PEA146-152
 		  1A:116-122
-
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_PEA233-242
 		  1B:203-212
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_PEA146-152
 		  1-
C:116-122
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_PEA233-242
 		  1-
D:203-212
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_PEA146-152
 		  2A:116-122
C:116-122
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_PEA233-242
 		  2B:203-212
D:203-212

(-) Exons   (0, 0)

(no "Exon" information available for 1BQP)

(-) 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:181
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:181
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN 211
               SCOP domains d1bqp.1 A:,B: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1bqpA00 A:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee....eeee......eeeeee...ee..........eeeeeeeeeee.........eeeeeee........hhhhh........hhhhh.eeeeee..............eeeeee......eeee........eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bqp A   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain B from PDB  Type:PROTEIN  Length:47
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:47
                                   227       237       247       257       
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 264
               SCOP domains d1bqp.1 A:,B: Legume lectin                     SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhh..eeeeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1bqp B 188 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 234
                                   197       207       217       227       


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:181
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN 211
               SCOP domains d1bqp.2 C:,D: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1bqpC00 C:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee....eeee......eeeeee...ee.ee....ee.eeeeeeeeeee.........eeeeeeee.......hhhhh........hhhhh.eeeeee..............eeeeee......eeee........eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bqp C   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain D from PDB  Type:PROTEIN  Length:47
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:47
                                   227       237       247       257       
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 264
               SCOP domains d1bqp.2 C:,D: Legume lectin                     SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhh..eeeeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1bqp D 188 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 234
                                   197       207       217       227
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LEC_PEA | P02867)
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:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ 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:80 - Asp A:81   [ RasMol ]  
    Ala C:80 - Asp C:81   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 ](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
  1bqp
    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
  LEC_PEA | P02867
    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
  LEC_PEA | P02867
    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
        LEC_PEA | P02867: 1hkd 1ofs 1rin 2bqp 2ltn

(-) Related Entries Specified in the PDB File

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