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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 1.9 ANGSTROMS RESOLUTION OF ISOLECTIN I FROM THE SEEDS OF LATHYRUS OCHRUS
 
Authors :  Y. Bourne, C. Cambillau
Date :  27 Jan 93  (Deposition) - 30 Apr 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Bourne, C. Abergel, C. Cambillau, M. Frey, P. Rouge, J. C. Fontecilla-Camps
X-Ray Crystal Structure Determination And Refinement At 1. 9 A Resolution Of Isolectin I From The Seeds Of Lathyrus Ochrus.
J. Mol. Biol. V. 214 571 1990
PubMed-ID: 2380988  |  Reference-DOI: 10.1016/0022-2836(90)90199-V

(-) Compounds

Molecule 1 - LEGUME ISOLECTIN I (ALPHA CHAIN)
    ChainsA, C
    EngineeredYES
    OrganSEED
    Organism CommonYELLOW-FLOWERED PEA
    Organism ScientificLATHYRUS OCHRUS
    Organism Taxid3858
 
Molecule 2 - LEGUME ISOLECTIN I (BETA CHAIN)
    ChainsB, D
    EngineeredYES
    OrganSEED
    Organism CommonYELLOW-FLOWERED PEA
    Organism ScientificLATHYRUS OCHRUS
    Organism Taxid3858

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:750 , HOH A:751BINDING SITE FOR RESIDUE CA A 227
2AC2SOFTWAREGLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:752 , HOH A:753BINDING SITE FOR RESIDUE MN A 228
3AC3SOFTWAREASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:768 , HOH C:769BINDING SITE FOR RESIDUE CA C 457
4AC4SOFTWAREGLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:770 , HOH C:771BINDING SITE FOR RESIDUE MN C 458

(-) SS Bonds  (0, 0)

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

(-) 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  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LECB_LATOC_001 *Q16PLECB_LATOC  ---  ---A/CQ16P
2UniProtVAR_LECB_LATOC_002 *S66ALECB_LATOC  ---  ---A/CS66A
3UniProtVAR_LECB_LATOC_003 *A168GLECB_LATOC  ---  ---A/CA168G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LECB_LATOC_001 *Q16PLECB_LATOC  ---  ---A/CQ16P
2UniProtVAR_LECB_LATOC_002 *S66ALECB_LATOC  ---  ---A/CS66A
3UniProtVAR_LECB_LATOC_003 *A168GLECB_LATOC  ---  ---A/CA168G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LECB_LATOC_001 *Q16PLECB_LATOC  ---  ---CQ16P
2UniProtVAR_LECB_LATOC_002 *S66ALECB_LATOC  ---  ---CS66A
3UniProtVAR_LECB_LATOC_003 *A168GLECB_LATOC  ---  ---CA168G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LECB_LATOC_001 *Q16PLECB_LATOC  ---  ---AQ16P
2UniProtVAR_LECB_LATOC_002 *S66ALECB_LATOC  ---  ---AS66A
3UniProtVAR_LECB_LATOC_003 *A168GLECB_LATOC  ---  ---AA168G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_LATOC16-25
 
  2B:16-25
D:16-25
2LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECB_LATOC116-122
 
  2A:116-122
C:116-122
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_LATOC16-25
 
  2B:16-25
D:16-25
2LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECB_LATOC116-122
 
  2A:116-122
C:116-122
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_LATOC16-25
 
  1-
D:16-25
2LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECB_LATOC116-122
 
  1-
C:116-122
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC1_LATOC16-25
 
  1B:16-25
-
2LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECB_LATOC116-122
 
  1A:116-122
-

(-) Exons   (0, 0)

(no "Exon" information available for 1LOE)

(-) 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:180
 aligned with LECB_LATOC | P04122 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           LECB_LATOC     1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWKLQNGKEANVVIAFNAATNVLTVSLTYP 180
               SCOP domains d1loe.1 A:,B: Legume lectin                                                                                                                                                          SCOP domains
               CATH domains 1loeA00 A:1-180  [code=2.60.120.200, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh........hhhhh.eeeeee..............eeeeee......eeee............................. Sec.struct. author
                 SAPs(SNPs) ---------------P-------------------------------------------------A-----------------------------------------------------------------------------------------------------G------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1loe A   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWALQNGKEANVVIAFNAATNVLTVSLTYP 180
                                    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:46
 aligned with LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:46
                                    11        21        31        41      
           LEC1_LATOC     2 TSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELA  47
               SCOP domains d1loe.1 A:,B: Legume lectin                    SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE --------------LECTIN_LEG---------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1loe B   2 TSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELA  47
                                    11        21        31        41      

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with LECB_LATOC | P04122 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           LECB_LATOC     1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWKLQNGKEANVVIAFNAATNVLTVSLTYPN 181
               SCOP domains d1loe.2 C:,D: Legume lectin                                                                                                                                                           SCOP domains
               CATH domains 1loeC00 C:1-181  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) -Lectin_legB-1loeC01 C:2-181                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -Lectin_legB-1loeC02 C:2-181                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh..............eeeeee..............eeeeee......eeee.............................. Sec.struct. author
                 SAPs(SNPs) ---------------P-------------------------------------------------A-----------------------------------------------------------------------------------------------------G------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1loe C   1 TETTSFSITKFGPDQQNLIFQGDGYTTKERLTLTKAVRNTVGRALYSSPIHIWDSKTGNVANFVTSFTFVIDAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSKDYDKTSQTVAVEFDTFYNTAWDPSNGDRHIGIDVNSIKSINTKSWALQNGKEANVVIAFNAATNVLTVSLTYPN 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 LEC1_LATOC | P12306 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:47
                                    10        20        30        40       
           LEC1_LATOC     1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWFFHSELA  47
               SCOP domains d1loe.2 C:,D: Legume lectin                     SCOP domains
               CATH domains ----------------------------------------------- CATH domains
           Pfam domains (1) Lectin_legB-1loeD01 D:1-43                 ---- Pfam domains (1)
           Pfam domains (2) Lectin_legB-1loeD02 D:1-43                 ---- Pfam domains (2)
         Sec.struct. author ..........hhhhhh..eeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1loe D   1 ETSYTLNEVVPLKEFVPEWVRIGFSATTGAEFAAHEVLSWYFHSELA  47
                                    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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (3, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (LECB_LATOC | P04122)
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.

Chain B,D   (LEC1_LATOC | P12306)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEC1_LATOC | P123061loa 1lob 1loc 1lod 1lof 1log
        LECB_LATOC | P041221lgb 1lgc 1loa 1lob 1loc 1lod 1lof 1log

(-) Related Entries Specified in the PDB File

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