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(-) Description

Title :  IMPROVED STRUCTURE OF PHYTOHEMAGGLUTININ-L FROM THE KIDNEY BEAN
 
Authors :  L. Buts, T. W. Hamelryck, M. Dao-Thi, R. Loris, L. Wyns, M. E. Etzler
Date :  21 Nov 00  (Deposition) - 13 Dec 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Jelly-Roll Fold, Legume Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Buts, M. H. Dao-Thi, R. Loris, L. Wyns, M. Etzler, T. Hamelryck
Weak Protein-Protein Interactions In Lectins: The Crystal Structure Of A Vegetative Lectin From The Legume Dolichos Biflorus.
J. Mol. Biol. V. 309 193 2001
PubMed-ID: 11491289  |  Reference-DOI: 10.1006/JMBI.2001.4639
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ
    Chains: A, B, C, D
    Fragment: LEUCOAGGLUTINATING FRACTION OF THE SEED LECTIN
    Organ: SEED
    Organism Scientific: PHASEOLUS VULGARIS
    Organism Taxid: 3885

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MN4Ligand/IonMANGANESE (II) ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:12 , GLU A:13 , SER A:25 , GLU B:201 , TRP B:202BINDING SITE FOR RESIDUE NAG A 259
02AC2SOFTWAREGLU A:201 , TRP A:202 , ASN B:12 , GLU B:13 , VAL B:24 , SER B:25BINDING SITE FOR RESIDUE NAG B 259
03AC3SOFTWAREASN C:12 , GLU C:13 , VAL C:24 , SER C:25 , GLU D:201 , TRP D:202BINDING SITE FOR RESIDUE NAG C 259
04AC4SOFTWAREGLU C:201 , TRP C:202 , PHE D:11 , ASN D:12 , GLU D:13 , SER D:25BINDING SITE FOR RESIDUE NAG D 259
05AC5SOFTWAREGLU A:122 , ASP A:124 , ASP A:132 , HIS A:137 , HOH A:1254 , HOH A:1255BINDING SITE FOR RESIDUE MN A 253
06AC6SOFTWAREASP A:124 , LEU A:126 , ASN A:128 , ASP A:132 , HOH A:1257 , HOH A:1258BINDING SITE FOR RESIDUE CA A 256
07AC7SOFTWAREGLU B:122 , ASP B:124 , ASP B:132 , HIS B:137 , HOH B:2254 , HOH B:2255BINDING SITE FOR RESIDUE MN B 253
08AC8SOFTWAREASP B:124 , LEU B:126 , ASN B:128 , ASP B:132 , HOH B:2257 , HOH B:2258BINDING SITE FOR RESIDUE CA B 256
09AC9SOFTWAREGLU C:122 , ASP C:124 , ASP C:132 , HIS C:137 , HOH C:3254 , HOH C:3255BINDING SITE FOR RESIDUE MN C 253
10BC1SOFTWAREASP C:124 , LEU C:126 , ASN C:128 , ASP C:132 , HOH C:3257 , HOH C:3258BINDING SITE FOR RESIDUE CA C 256
11BC2SOFTWAREGLU D:122 , ASP D:124 , ASP D:132 , HIS D:137 , HOH D:4254 , HOH D:4255BINDING SITE FOR RESIDUE MN D 253
12BC3SOFTWAREASP D:124 , LEU D:126 , ASN D:128 , ASP D:132 , HOH D:4257 , HOH D:4258BINDING SITE FOR RESIDUE CA D 256

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G8W)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:85 -Asp A:86
2Ala B:85 -Asp B:86
3Ala C:85 -Asp C:86
4Ala D:85 -Asp D:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G8W)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.PHAL_PHAVU139-145
 
 
 		  4A:119-125
B:119-125
C:119-125
D:119-125
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.PHAL_PHAVU219-228
 
 
 		  4A:199-208
B:199-208
C:199-208
D:199-208

(-) Exons   (0, 0)

(no "Exon" information available for 1G8W)

(-) 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 PHAL_PHAVU | P05087 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           PHAL_PHAVU    21 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 253
               SCOP domains d1g8wa_ A: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                      SCOP domains
               CATH domains 1g8wA00 A:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.........eeeeeeeeee..........eeeeeeeee.......hhhhh............eeeeee............eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8w A   1 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 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 PHAL_PHAVU | P05087 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           PHAL_PHAVU    21 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 253
               SCOP domains d1g8wb_ B: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                      SCOP domains
               CATH domains 1g8wB00 B:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.........eeeeeeeeee..........eeeeeeeee.......hhhhh............eeeeee............eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8w B   1 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 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 PHAL_PHAVU | P05087 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           PHAL_PHAVU    21 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 253
               SCOP domains d1g8wc_ C: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                      SCOP domains
               CATH domains 1g8wC00 C:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.........eeeeeeeeee..........eeeeeeeee.......hhhhh............eeeeee............eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8w C   1 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 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 PHAL_PHAVU | P05087 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           PHAL_PHAVU    21 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 253
               SCOP domains d1g8wd_ D: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                                                      SCOP domains
               CATH domains 1g8wD00 D:1-233  [code=2.60.120.200, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhh.eeeee..ee.....ee..............eeeeee...ee.........eeeeeeeeee..........eeeeeeeee.......hhhhh............eeeeee............eeeeee.......eee........eeeeeeee....eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------LECTIN_-------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g8w D   1 SNDIYFNFQRFNETNLILQRDASVSSSGQLRLTNLNGNGEPRVGSLGRAFYSAPIQIWDNTTGTVASFATSFTFNIQVPNNAGPADGLAFALVPVGSQPKDKGGFLGLFDGSNSNFHTVAVEFDTLYNKDWDPTERHIGIDVNSIRSIKTTRWDFVNGENAEVLITYDSSTNLLVASLVYPSQKTSFIVSDTVDLKSVLPEWVSVGFSATTGINKGNVETNDVLSWSFASKLS 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)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 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 1G8W)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PHAL_PHAVU | P05087)
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.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.

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  1g8w
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHAL_PHAVU | P05087: 1fat

(-) Related Entries Specified in the PDB File

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