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(-) Description

Title :  THE STRUCTURE OF THE PEA LECTIN-D-GLUCOPYRANOSE COMPLEX
 
Authors :  S. N. Ruzeinikov, I. Mikhailova Yu, I. N. Tsygannik, W. Pangborn, W. Duax, V. Z. Pletnev
Date :  08 Dec 98  (Deposition) - 16 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pea Lectin, D-Glucopyranose Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Z. Pletnev, S. N. Ruzheinikov, I. N. Tsygannik, I. Mikhailova Yu, W. Duax, D. Ghosh, W. Pangborn
The Structure Of Pea Lectin-D-Glucopyranose Complex At A 1. 9 A Resolution
Russ. J. Bioorganic Chem. V. 23 469 1997
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PEA LECTIN)
    Chains: A, B
    Organ: SEEDS
    Organism Common: PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GLC2Ligand/IonALPHA-D-GLUCOSE
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , ASP A:81 , GLY A:99 , PHE A:123 , ASN A:125 , GLY A:216 , ALA A:217 , GLU A:218BINDING SITE FOR RESIDUE GLC A 337
2AC2SOFTWAREALA B:80 , ASP B:81 , GLY B:98 , GLY B:99 , PHE B:123 , ASN B:125 , ALA B:169 , GLY B:216 , ALA B:217 , GLU B:218 , HOH B:412BINDING SITE FOR RESIDUE GLC B 338
3AC3SOFTWAREASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:397 , HOH A:419BINDING SITE FOR RESIDUE CA A 235
4AC4SOFTWAREGLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:347 , HOH A:358BINDING SITE FOR RESIDUE MN A 236
5AC5SOFTWAREASP B:121 , PHE B:123 , ASN B:125 , ASP B:129 , HOH B:358 , HOH B:360BINDING SITE FOR RESIDUE CA B 235
6AC6SOFTWAREGLU B:119 , ASP B:121 , ASP B:129 , HIS B:136 , HOH B:359 , HOH B:365BINDING SITE FOR RESIDUE MN B 236
7CB1AUTHORASP A:81 , GLY A:99 , ASN A:125 , ALA A:217 , GLU A:218CARBOHYDRATE-BINDING SITE OF THE FIRST MONOMER.
8CB2AUTHORASP B:81 , GLY B:99 , ASN B:125 , ALA B:217 , GLU B:218CARBOHYDRATE-BINDING SITE OF THE SECOND MONOMER.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BQP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:80 -Asp A:81
2Ala B:80 -Asp B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BQP)

(-) PROSITE Motifs  (2, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BQP)

(-) 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:228
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:234
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPNSLEEENVTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 264
               SCOP domains d2bqpa_ A: Legume lectin                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bqpA00 A:1-234  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........eeeee.eeeee..eeeee....eeeeeeeeeeeeee.........eeeeeeeeeeee........eeeeeee.........hhh..........hhh.eeeeeee.............eeeeeeee.....eeeee.......eeeeeeee....eeeeeeee..------.eeeeeeeee.hhh...eeeeeeeeeeee.eeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_--------------------------------------------------------------------------------LECTIN_LEG---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bqp A   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN------VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      190       200       210       220       230    
                                                                                                                                                                                                              181    188                                              


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:234
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPNSLEEENVTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 264
               SCOP domains d2bqpb_ B: Legume lectin                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bqpB00 B:1-234  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee........eeeee.eeeee..eeeee....eeeeeeeeeeeeee.........eeeeeeeeeeee........eeeeeee.........hhh..........hhh.eeeeeee.............eeeeeeee.....eeeee.......eeeeeeee....eeeeeeee..------.eeeeeeeee.hhhh..eeeeeeeeeeee.eeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_--------------------------------------------------------------------------------LECTIN_LEG---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bqp B   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPN------VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|      190       200       210       220       230    
                                                                                                                                                                                                              181    188
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BQP)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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  2bqp
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 Related Entries

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

UniProtKB/Swiss-Prot
        LEC_PEA | P02867: 1bqp 1hkd 1ofs 1rin 2ltn

(-) Related Entries Specified in the PDB File

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