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(-) Description

Title :  STRUCTURE OF PEA LECTIN IN COMPLEX WITH ALPHA-METHYL-D-GLUCOPYRANOSIDE
 
Authors :  M. B. Shevtsov, I. N. Tsygannik
Date :  06 Mar 03  (Deposition) - 18 Mar 03  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Plant Lectin, Carbohydrate Binding Protein, Calcium, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shevtsov, I. N. Tsygannik
Structure Of Pea Lectin In Complex With Alpha-Methyl-D-Glucopyranoside
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEA LECTIN ALPHA CHAIN
    Chains: A, C
    Fragment: RESIDUES 31-211
    Organ: SEEDS
    Organism Common: GARDEN PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888
    Other Details: ALPHA-METHYL-D-GLUCOPYRANOSIDE IS PRESENT IN TWO BINDING SITES OF MOLECULE
 
Molecule 2 - PEA LECTIN BETA CHAIN
    Chains: B, D
    Fragment: RESIDUES 218-269
    Organ: SEEDS
    Organism Common: GARDEN PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888
    Other Details: ALPHA-METHYL-D-GLUCOPYRANOSIDE IS PRESENT IN TWO BINDING SITES OF MOLECULE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GYP2Ligand/IonMETHYL-ALPHA-D-GLUCOPYRANOSIDE
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:80 , ASP A:81 , GLY A:99 , PHE A:123 , ASN A:125 , HOH A:2128 , GLY B:29 , ALA B:30 , GLU B:31BINDING SITE FOR RESIDUE GYP A1184
2AC2SOFTWAREALA C:80 , ASP C:81 , GLY C:98 , GLY C:99 , PHE C:123 , ASN C:125 , GLY D:29 , ALA D:30 , GLU D:31BINDING SITE FOR RESIDUE GYP C1184
3AC3SOFTWAREASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:2060 , HOH A:2077BINDING SITE FOR RESIDUE CA A1182
4AC4SOFTWAREGLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE MN A1183
5AC5SOFTWAREASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:2049 , HOH C:2060BINDING SITE FOR RESIDUE CA C1182
6AC6SOFTWAREGLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:2106 , HOH C:2107BINDING SITE FOR RESIDUE MN C1183

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 1HKD)

(-) 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
C:116-122
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_PEA233-242
 		  2B:16-25
D:16-25

(-) Exons   (0, 0)

(no "Exon" information available for 1HKD)

(-) 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: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 d1hkd.1 A:,B: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1hkdA00 A:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..eee..eeeee......eeeeee...ee..........eeeeeeeeeee.........eeeeeeee.......hhhhh..............eeeeee..............eeeeee......eeee........eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkd 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:49
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:49
                                   227       237       247       257         
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT 266
               SCOP domains d1hkd.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
                 1hkd B   1 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT  49
                                    10        20        30        40         


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 d1hkd.2 C:,D: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1hkdC00 C:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh........hhhhh.eeeeee..............eeeeee......eeee.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkd 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:49
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:49
                                   227       237       247       257         
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT 266
               SCOP domains d1hkd.2 C:,D: Legume lectin                       SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh...eeeeeeeee......eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG------------------------ PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1hkd D   1 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT  49
                                    10        20        30        40
   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 1HKD)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological 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.

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  Cis Peptide Bonds
    Ala A:80 - Asp A:81   [ RasMol ]  
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1bqp THE STRUCTURE OF THE PEA LECTIN-D- MANNOPYRANOSE COMPLEX
1rin PEA LECTIN COMPLEX WITH METHYL-3,6-DI-O - (ALPHA-D-MANNOPYRANOSYL)- ALPHA-D- MANNOPYRANOSIDE
2bqp THE STRUCTURE OF THE PEA LECTIN-D- GLUCOPYRANOSE COMPLEX
2ltn