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(-) Description

Title :  ISOLECTIN B4 FROM VICIA VILLOSA IN COMPLEX WITH THE TN ANTIGEN
 
Authors :  A. Babino, D. Tello, A. Rojas, S. Bay, E. Osinaga, P. M. Alzari
Date :  30 Oct 02  (Deposition) - 25 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cancer Antigen, Vicia Villosa Lectin, Glycoprotein Tn-Binding Protein, Carbohydrate Recognition, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Babino, D. Tello, A. Rojas, S. Bay, E. Osinaga, P. M. Alzari
The Crystal Structure Of A Plant Lectin In Complex With The Tn Antigen
Febs Lett. V. 536 106 2003
PubMed-ID: 12586347  |  Reference-DOI: 10.1016/S0014-5793(03)00037-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOLECTIN B4
    Chains: A, B, C, D
    Organism Common: HAIRY VETCH
    Organism Scientific: VICIA VILLOSA
    Organism Taxid: 3911
    Other Details: EXTRACTED FROM SEEDS
    Tissue: SEED

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric/Biological Unit (5, 24)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FUC4Ligand/IonALPHA-L-FUCOSE
3MN4Ligand/IonMANGANESE (II) ION
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5TNR4Ligand/IonO-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:61 , GLU A:201 , FUC A:302 , NAG A:303BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARENAG A:301 , NAG A:303 , PRO B:13 , ASN B:14BINDING SITE FOR RESIDUE FUC A 302
03AC3SOFTWARENAG A:301 , FUC A:302BINDING SITE FOR RESIDUE NAG A 303
04AC4SOFTWAREASN B:61 , GLU B:201 , FUC B:302 , NAG B:303BINDING SITE FOR RESIDUE NAG B 301
05AC5SOFTWAREPRO A:13 , ASN A:14 , NAG B:301 , NAG B:303BINDING SITE FOR RESIDUE FUC B 302
06AC6SOFTWARENAG B:301 , FUC B:302BINDING SITE FOR RESIDUE NAG B 303
07AC7SOFTWAREASN C:61 , GLU C:201 , FUC C:302 , NAG C:303BINDING SITE FOR RESIDUE NAG C 301
08AC8SOFTWARENAG C:301 , NAG C:303 , ASN D:14BINDING SITE FOR RESIDUE FUC C 302
09AC9SOFTWARENAG C:301 , FUC C:302BINDING SITE FOR RESIDUE NAG C 303
10BC1SOFTWAREASN D:61 , GLU D:201 , FUC D:302 , NAG D:303BINDING SITE FOR RESIDUE NAG D 301
11BC2SOFTWAREPRO C:13 , ASN C:14 , NAG D:301BINDING SITE FOR RESIDUE FUC D 302
12BC3SOFTWARENAG D:301BINDING SITE FOR RESIDUE NAG D 303
13BC4SOFTWAREASP A:125 , TYR A:127 , ASN A:129 , ASP A:132 , HOH A:1403BINDING SITE FOR RESIDUE CA A 252
14BC5SOFTWAREGLU A:123 , ASP A:125 , ASP A:132 , HIS A:137 , HOH A:1407 , HOH A:1408BINDING SITE FOR RESIDUE MN A 253
15BC6SOFTWAREASP B:125 , TYR B:127 , ASN B:129 , ASP B:132 , HOH B:2405 , HOH B:2410BINDING SITE FOR RESIDUE CA B 252
16BC7SOFTWAREGLU B:123 , ASP B:125 , ASP B:132 , HIS B:137 , HOH B:2409 , HOH B:2415BINDING SITE FOR RESIDUE MN B 253
17BC8SOFTWAREASP C:125 , TYR C:127 , ASN C:129 , ASP C:132 , HOH C:3402 , HOH C:3414BINDING SITE FOR RESIDUE CA C 252
18BC9SOFTWAREGLU C:123 , ASP C:125 , ASP C:132 , HIS C:137 , HOH C:3413 , HOH C:3418BINDING SITE FOR RESIDUE MN C 253
19CC1SOFTWAREASP D:125 , TYR D:127 , ASN D:129 , ASP D:132 , HOH D:4413BINDING SITE FOR RESIDUE CA D 252
20CC2SOFTWAREGLU D:123 , ASP D:125 , ASP D:132 , HIS D:137 , HOH D:4411 , HOH D:4414BINDING SITE FOR RESIDUE MN D 253
21CC3SOFTWAREASP A:85 , GLY A:103 , TYR A:127 , ASN A:129 , LEU A:213 , ASN A:214 , VAL A:217BINDING SITE FOR RESIDUE TNR A 1401
22CC4SOFTWAREASP B:85 , GLY B:103 , TYR B:127 , ASN B:129 , GLY B:212 , LEU B:213 , ASN B:214 , VAL B:217BINDING SITE FOR RESIDUE TNR B 2401
23CC5SOFTWAREASN A:134 , ASP C:85 , GLY C:102 , GLY C:103 , TYR C:127 , ASN C:129 , GLY C:212 , LEU C:213 , ASN C:214 , VAL C:217 , HOH C:3409BINDING SITE FOR RESIDUE TNR C 3401
24CC6SOFTWAREGLU B:146 , ASP D:85 , GLY D:102 , GLY D:103 , ASN D:129 , GLY D:212 , LEU D:213 , ASN D:214 , HOH D:4403BINDING SITE FOR RESIDUE TNR D 4401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N47)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:84 -Asp A:85
2Ala B:84 -Asp B:85
3Ala C:84 -Asp C:85
4Ala D:84 -Asp D:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N47)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_VICVI108-114
 
 
 		  4A:120-126
B:120-126
C:120-126
D:120-126
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_VICVI163-172
 
 
 		  4A:199-208
B:199-208
C:199-208
D:199-208

(-) Exons   (0, 0)

(no "Exon" information available for 1N47)

(-) 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:233
 aligned with LEC_VICVI | P56625 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:233
                                                              36 37        47         48                                                                                                  149          150       160          161                     185            
                                    10        20        30     |  38        |-        48        58        68        78        88        98       108       118       128       138       148|        -   |   156   |     -      |164       174       184|        -   
            LEC_VICVI     1 SESTSFSFTNFNPNQENLILQEDALVNSKGTLELTK--NGKPVPESLGR----------NCTTLASFTTSFSFVMSAPNSLDVADGLAFFLAPPDTQPQKRGGFLGLFKDRKHDISYQSVAVEFDTYSNVWDPNTTHIGIDTNTIESKKITPFDMVYGEKI------------LFASLVFPVSQ------------DILPEYVRVGFSATTGLNEGVVETH------------   -
               SCOP domains d1n47a_ A: Legume lectin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n47A00 A:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.............eeeeee...ee........eeeeeeeee..........eeeeeeee........hhhhh........hhhhh.eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n47 A   1 TESTSFSFTNFNPNQNNLILQEDALVNSAGTLELTAVAAGAPVPDSLGRALYAAPIHIHDNTTLASFTTSFSFVMAAPAAAAVADGLAFFLAPPDTQPQARGGFLGLFADRAHDASYQTVAVEFDTYSNAWDPNYTHIGIDTNGIESKKTTPFDMVYGEKANIVITYQASTKALAASLVFPVSQTSYAVSARVDLRDILPEYVRVGFSATTGLNAGVVETHDIVSWSFAVSLA 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with LEC_VICVI | P56625 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:233
                                                              36 37        47         48                                                                                                  149          150       160          161                     185            
                                    10        20        30     |  38        |-        48        58        68        78        88        98       108       118       128       138       148|        -   |   156   |     -      |164       174       184|        -   
            LEC_VICVI     1 SESTSFSFTNFNPNQENLILQEDALVNSKGTLELTK--NGKPVPESLGR----------NCTTLASFTTSFSFVMSAPNSLDVADGLAFFLAPPDTQPQKRGGFLGLFKDRKHDISYQSVAVEFDTYSNVWDPNTTHIGIDTNTIESKKITPFDMVYGEKI------------LFASLVFPVSQ------------DILPEYVRVGFSATTGLNEGVVETH------------   -
               SCOP domains d1n47b_ B: Legume lectin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n47B00 B:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.............eeeeee...ee........eeeeeeeee..........eeeeeeee........hhhhh........hhhhh.eeeeee...........eeeeee......eeee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n47 B   1 TESTSFSFTNFNPNQNNLILQEDALVNSAGTLELTAVAAGAPVPDSLGRALYAAPIHIHDNTTLASFTTSFSFVMAAPAAAAVADGLAFFLAPPDTQPQARGGFLGLFADRAHDASYQTVAVEFDTYSNAWDPNYTHIGIDTNGIESKKTTPFDMVYGEKANIVITYQASTKALAASLVFPVSQTSYAVSARVDLRDILPEYVRVGFSATTGLNAGVVETHDIVSWSFAVSLA 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain C from PDB  Type:PROTEIN  Length:233
 aligned with LEC_VICVI | P56625 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:233
                                                              36 37        47         48                                                                                                  149          150       160          161                     185            
                                    10        20        30     |  38        |-        48        58        68        78        88        98       108       118       128       138       148|        -   |   156   |     -      |164       174       184|        -   
            LEC_VICVI     1 SESTSFSFTNFNPNQENLILQEDALVNSKGTLELTK--NGKPVPESLGR----------NCTTLASFTTSFSFVMSAPNSLDVADGLAFFLAPPDTQPQKRGGFLGLFKDRKHDISYQSVAVEFDTYSNVWDPNTTHIGIDTNTIESKKITPFDMVYGEKI------------LFASLVFPVSQ------------DILPEYVRVGFSATTGLNEGVVETH------------   -
               SCOP domains d1n47c_ C: Legume lectin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n47C00 C:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.............eeeeee...ee........eeeeeeeee..........eeeeeeee........hhhhh..............eeeeee...........eeeeee......eeee........eeeeeee.....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n47 C   1 TESTSFSFTNFNPNQNNLILQEDALVNSAGTLELTAVAAGAPVPDSLGRALYAAPIHIHDNTTLASFTTSFSFVMAAPAAAAVADGLAFFLAPPDTQPQARGGFLGLFADRAHDASYQTVAVEFDTYSNAWDPNYTHIGIDTNGIESKKTTPFDMVYGEKANIVITYQASTKALAASLVFPVSQTSYAVSARVDLRDILPEYVRVGFSATTGLNAGVVETHDIVSWSFAVSLA 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   


Chain D from PDB  Type:PROTEIN  Length:233
 aligned with LEC_VICVI | P56625 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:233
                                                              36 37        47         48                                                                                                  149          150       160          161                     185            
                                    10        20        30     |  38        |-        48        58        68        78        88        98       108       118       128       138       148|        -   |   156   |     -      |164       174       184|        -   
            LEC_VICVI     1 SESTSFSFTNFNPNQENLILQEDALVNSKGTLELTK--NGKPVPESLGR----------NCTTLASFTTSFSFVMSAPNSLDVADGLAFFLAPPDTQPQKRGGFLGLFKDRKHDISYQSVAVEFDTYSNVWDPNTTHIGIDTNTIESKKITPFDMVYGEKI------------LFASLVFPVSQ------------DILPEYVRVGFSATTGLNEGVVETH------------   -
               SCOP domains d1n47d_ D: Legume lectin                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n47D00 D:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee.............eeeeee...ee........eeeeeeeee..........eeeeeeee........hhhhh........hhhhh.eeeeee...........eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhh...eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n47 D   1 TESTSFSFTNFNPNQNNLILQEDALVNSAGTLELTAVAAGAPVPDSLGRALYAAPIHIHDNTTLASFTTSFSFVMAAPAAAAVADGLAFFLAPPDTQPQARGGFLGLFADRAHDASYQTVAVEFDTYSNAWDPNYTHIGIDTNGIESKKTTPFDMVYGEKANIVITYQASTKALAASLVFPVSQTSYAVSARVDLRDILPEYVRVGFSATTGLNAGVVETHDIVSWSFAVSLA 233
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 1N47)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LEC_VICVI | P56625)
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.

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  Cis Peptide Bonds
    Ala A:84 - Asp A:85   [ RasMol ]  
    Ala B:84 - Asp B:85   [ RasMol ]  
    Ala C:84 - Asp C:85   [ RasMol ]  
    Ala D:84 - Asp D:85   [ RasMol ]  
 

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  1n47
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 Related Entries

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

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