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(-) Description

Title :  PARKIA PLATYCEPHALA SEED LECTIN IN COMPLEX WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
 
Authors :  F. Gallego Del Sol, B. S. Cavada, J. J. Calvete
Date :  22 Apr 05  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Prism, Lectin, X-Man, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Gallego Del Sol, C. Nagano, B. S. Cavada, J. J. Calvete
The First Crystal Structure Of A Mimosoideae Lectin Reveals A Novel Quaternary Arrangement Of A Widespread Domain.
J. Mol. Biol. V. 353 574 2005
PubMed-ID: 16185708  |  Reference-DOI: 10.1016/J.JMB.2005.08.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE/GLUCOSE-SPECIFIC LECTIN
    ChainsA, B
    Organism ScientificPARKIA PLATYCEPHALA
    Organism Taxid185447
    TissueSEEDS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1XMM6Ligand/Ion(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:310 , GLY A:311 , PHE A:388 , GLY A:431 , ASP A:432 , TYR A:433 , ASP A:435 , HOH A:555 , XMM B:453BINDING SITE FOR RESIDUE XMM A 450
2AC2SOFTWAREALA A:163 , GLY A:164 , ASP A:165 , PHE A:239 , GLY A:282 , TYR A:283 , TYR A:284 , ASP A:286 , HOH A:541BINDING SITE FOR RESIDUE XMM A 451
3AC3SOFTWAREGLY A:16 , ARG A:60 , GLY A:136 , TYR A:137 , TYR A:138 , ASP A:140 , ASP B:386 , XMM B:455BINDING SITE FOR RESIDUE XMM A 452
4AC4SOFTWAREASP A:386 , XMM A:450 , GLY B:16 , ARG B:60 , GLY B:136 , TYR B:137 , TYR B:138 , ASP B:140BINDING SITE FOR RESIDUE XMM B 453
5AC5SOFTWAREALA B:163 , GLY B:164 , ASP B:165 , PHE B:239 , GLY B:282 , TYR B:283 , TYR B:284 , ASP B:286 , HOH B:546BINDING SITE FOR RESIDUE XMM B 454
6AC6SOFTWAREASN A:90 , XMM A:452 , GLY B:310 , GLY B:311 , PHE B:388 , GLY B:431 , ASP B:432 , TYR B:433 , ASP B:435 , HOH B:553BINDING SITE FOR RESIDUE XMM B 455

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Gly A:9 -Pro A:10
2Trp A:74 -Pro A:75
3Gly A:108 -Pro A:109
4Gly A:157 -Pro A:158
5Gly A:255 -Pro A:256
6Gly A:304 -Pro A:305
7Trp A:367 -Pro A:368
8Gly A:404 -Pro A:405
9Gly B:9 -Pro B:10
10Trp B:74 -Pro B:75
11Gly B:108 -Pro B:109
12Gly B:157 -Pro B:158
13Gly B:255 -Pro B:256
14Gly B:304 -Pro B:305
15Trp B:367 -Pro B:368
16Gly B:404 -Pro B:405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LEC_PARPC_001 *I70VLEC_PARPC  ---  ---A/BI70V
2UniProtVAR_LEC_PARPC_002 *K227RLEC_PARPC  ---  ---A/BK227R
3UniProtVAR_LEC_PARPC_003 *D296NLEC_PARPC  ---  ---A/BD296N
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JACALIN_LECTINPS51752 Jacalin-type lectin domain profile.LEC_PARPC5-148
 
153-294
 
300-443
 
  6A:5-148
B:5-148
A:153-294
B:153-294
A:300-443
B:300-443

(-) Exons   (0, 0)

(no "Exon" information available for 1ZGS)

(-) 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:442
 aligned with LEC_PARPC | P83304 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:442
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  
            LEC_PARPC     3 KGMISVGPWGGSGGNYWSFKANHAITEIVIHVKDNIKSISFKDASGDISGTFGGKDPRENEKGDEKKIKIHWPTEYLKSISGSYGDYNGVLVIRSLSFITNLTTYGPFGSTSGGESFSIPIADSVVVGFHGRAGYYLDALGIFVQPVPHGTISFGPWGGPAGDDAFNFKVGSWIKDIIIYADAAINSIAFKDANGHCYGKFGGQDPNDIGVEKKVEIDGNLEHLKSISGTYGNYKGFEVVTSLSFITNVTKHGPFGIASGTSFSIPIEGSLVTGFHGKSGYYLDSIGIYVKPRDVEGSISIGPWGGSGGDPWSYTANEGINQIIIYAGSNIKSVAFKDTSGLDSATFGGVNPKDTGEKNTVSINWPSEYLTSISGTYGQYKFKDVFTTITSLSFTTNLATYGPFGKASATSFSIPIHNNMVVGFHGRAGDYLDAIGIFVKPD 444
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zgsA01 A:3-149  [code=2.100.10.30, no name defined]                                                                                               1zgsA02 A:150-295  [code=2.100.10.30, no name defined]                                                                                            1zgsA03 A:296-444  [code=2.100.10.30, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeeee....eeeeeeee...eeeeeeee........ee....hhhhh.eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee.....eee...ee.eeeeeeeeee...eeeeeeeeee.....eeeeeee.....eeeeee....eeeeeeee...eeeeeeee....eeeeee.........eeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eee...ee.eeeeeeeeee...eeeeeeeeee......eeeeeee....eeeeee....eeeeeeee...eeeeeeee........ee........eeeeee.......eeeeeeeeeeee...eeeeeeeeeeee...eeeeee....eee...ee.eeeeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --JACALIN_LECTIN  PDB: A:5-148 UniProt: 5-148                                                                                                     ----JACALIN_LECTIN  PDB: A:153-294 UniProt: 153-294                                                                                               -----JACALIN_LECTIN  PDB: A:300-443 UniProt: 300-443                                                                                                 - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgs A   3 KGMISVGPWGGSGGNYWSFKANHAITEIVIHVKDNIKSISFKDASGDISGTFGGKDPRENEKGDEKKIKIHWPTEYLKSISGSYGDYNGVLVIRSLSFITNLTTYGPFGSTSGGESFSIPIADSVVVGFHGRAGYYLDALGIFVQPVPHGTISFGPWGGPAGDDAFNFKVGSWIKDIIIYADAAINSIAFKDANGHCYGKFGGQDPNDIGVEKKVEIDGNLEHLKSISGTYGNYKGFEVVTSLSFITNVTKHGPFGIASGTSFSIPIEGSLVTGFHGKSGYYLDSIGIYVKPRDVEGSISIGPWGGSGGDPWSYTANEGINQIIIYAGSNIKSVAFKDTSGLDSATFGGVNPKDTGEKNTVSINWPSEYLTSISGTYGQYKFKDVFTTITSLSFTTNLATYGPFGKASATSFSIPIHNNMVVGFHGRAGDYLDAIGIFVKPD 444
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with LEC_PARPC | P83304 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:442
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  
            LEC_PARPC     3 KGMISVGPWGGSGGNYWSFKANHAITEIVIHVKDNIKSISFKDASGDISGTFGGKDPRENEKGDEKKIKIHWPTEYLKSISGSYGDYNGVLVIRSLSFITNLTTYGPFGSTSGGESFSIPIADSVVVGFHGRAGYYLDALGIFVQPVPHGTISFGPWGGPAGDDAFNFKVGSWIKDIIIYADAAINSIAFKDANGHCYGKFGGQDPNDIGVEKKVEIDGNLEHLKSISGTYGNYKGFEVVTSLSFITNVTKHGPFGIASGTSFSIPIEGSLVTGFHGKSGYYLDSIGIYVKPRDVEGSISIGPWGGSGGDPWSYTANEGINQIIIYAGSNIKSVAFKDTSGLDSATFGGVNPKDTGEKNTVSINWPSEYLTSISGTYGQYKFKDVFTTITSLSFTTNLATYGPFGKASATSFSIPIHNNMVVGFHGRAGDYLDAIGIFVKPD 444
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zgsB01 B:3-149  [code=2.100.10.30, no name defined]                                                                                               1zgsB02 B:150-295  [code=2.100.10.30, no name defined]                                                                                            1zgsB03 B:296-444  [code=2.100.10.30, no name defined]                                                                                                CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB01 B:311-443                                                                                                            - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB02 B:311-443                                                                                                            - Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB03 B:311-443                                                                                                            - Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB04 B:311-443                                                                                                            - Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB05 B:311-443                                                                                                            - Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Jacalin-1zgsB06 B:311-443                                                                                                            - Pfam domains (6)
         Sec.struct. author ...eeeeeee....eeeeee....eeeeeeee...eeeeeeee........ee....hhhhh.eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee.....eee...ee.eeeeeeeeee.....eeeeeeee.....eeeeeee.....eeeeee....eeeeeeee...eeeeeeee....eeeeee........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eee...ee.eeeeeeeeee...eeeeeeeeee......eeeeeee....eeeeee....eeeeeeee...eeeeeeee........ee........eeeeee.......eeeeeeeeeeee...eeeeeeeeeeee...eeeeee....eee...ee.eeeeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --JACALIN_LECTIN  PDB: B:5-148 UniProt: 5-148                                                                                                     ----JACALIN_LECTIN  PDB: B:153-294 UniProt: 153-294                                                                                               -----JACALIN_LECTIN  PDB: B:300-443 UniProt: 300-443                                                                                                 - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgs B   3 KGMISVGPWGGSGGNYWSFKANHAITEIVIHVKDNIKSISFKDASGDISGTFGGKDPRENEKGDEKKIKIHWPTEYLKSISGSYGDYNGVLVIRSLSFITNLTTYGPFGSTSGGESFSIPIADSVVVGFHGRAGYYLDALGIFVQPVPHGTISFGPWGGPAGDDAFNFKVGSWIKDIIIYADAAINSIAFKDANGHCYGKFGGQDPNDIGVEKKVEIDGNLEHLKSISGTYGNYKGFEVVTSLSFITNVTKHGPFGIASGTSFSIPIEGSLVTGFHGKSGYYLDSIGIYVKPRDVEGSISIGPWGGSGGDPWSYTANEGINQIIIYAGSNIKSVAFKDTSGLDSATFGGVNPKDTGEKNTVSINWPSEYLTSISGTYGQYKFKDVFTTITSLSFTTNLATYGPFGKASATSFSIPIHNNMVVGFHGRAGDYLDAIGIFVKPD 444
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  

   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  (0, 0)

(no "SCOP Domain" information available for 1ZGS)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
1aJacalin-1zgsB01B:311-443
1bJacalin-1zgsB02B:311-443
1cJacalin-1zgsB03B:311-443
1dJacalin-1zgsB04B:311-443
1eJacalin-1zgsB05B:311-443
1fJacalin-1zgsB06B:311-443

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEC_PARPC | P83304)
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:0005536    glucose binding    Interacting selectively and non-covalently with the D- or L-enantiomer of glucose.
    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:0000771    agglutination involved in conjugation    The aggregation or adhesion of compatible mating types via complementary cell-cell interactions prior to the formation of irreversible cellular contacts during conjugation.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEC_PARPC | P833041zgr

(-) Related Entries Specified in the PDB File

1zgr NATIVE PARKIA PLATYCEPHALA SEED LECTIN