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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1 COMPLEXED WITH GALACTOSE AT 1.6 A RESOLUTION
 
Authors :  G. Cioci, E. Mitchell, C. Gautier, M. Wimmerova, S. Perez, N. Gilboa-Ga A. Imberty
Date :  28 Jul 03  (Deposition) - 04 Dec 03  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sugar Binding Protein, Galactose Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Cioci, E. Mitchell, C. Gautier, M. Wimmerova, D. Sudakevitz, S. Perez, N. Gilboa-Garber, A. Imberty
Structural Basis Of Calcium And Galactose Recognition By The Lectin Pa-Il Of Pseudomonas Aeruginosa
Febs Lett. V. 555 297 2003
PubMed-ID: 14644431  |  Reference-DOI: 10.1016/S0014-5793(03)01249-3

(-) Compounds

Molecule 1 - PA-I GALACTOPHILIC LECTIN
    Chains: A, B, C, D
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PA-IL, GALACTOSE-BINDING LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GAL4Ligand/IonBETA-D-GALACTOSE
3GLA3Ligand/IonALPHA D-GALACTOSE
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:36 , HIS A:50 , GLN A:53 , ASP A:100 , THR A:104 , ASN A:107 , CA A:900 , HOH A:2069 , HOH A:2126 , HOH A:2127 , HOH A:2128 , HOH A:2129BINDING SITE FOR RESIDUE GAL A 901
02AC2SOFTWARETYR B:36 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:900 , HOH B:2054 , HOH B:2058 , HOH B:2099 , HOH B:2100 , HOH B:2101BINDING SITE FOR RESIDUE GLA B 901
03AC3SOFTWARETYR B:36 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:900 , HOH B:2054 , HOH B:2099 , HOH B:2100 , HOH B:2101BINDING SITE FOR RESIDUE GAL B 902
04AC4SOFTWARETYR C:36 , HIS C:50 , GLN C:53 , ASP C:100 , THR C:104 , ASN C:107 , CA C:900 , HOH C:2066 , HOH C:2116 , HOH C:2117 , HOH C:2118 , HOH C:2119 , HOH C:2120BINDING SITE FOR RESIDUE GLA C 901
05AC5SOFTWARETYR C:36 , HIS C:50 , GLN C:53 , ASP C:100 , THR C:104 , ASN C:107 , CA C:900 , HOH C:2116 , HOH C:2117 , HOH C:2119 , HOH C:2120BINDING SITE FOR RESIDUE GAL C 902
06AC6SOFTWAREHOH B:2050 , HOH B:2102 , TYR D:36 , HIS D:50 , GLN D:53 , ASP D:100 , THR D:104 , ASN D:107 , CA D:900 , HOH D:2065 , HOH D:2120 , HOH D:2121BINDING SITE FOR RESIDUE GLA D 901
07AC7SOFTWAREHOH B:2102 , TYR D:36 , HIS D:50 , GLN D:53 , ASP D:100 , THR D:104 , ASN D:107 , CA D:900 , HOH D:2065 , HOH D:2120BINDING SITE FOR RESIDUE GAL D 902
08AC8SOFTWARETYR A:36 , ASP A:100 , THR A:104 , ASN A:107 , ASN A:108 , GAL A:901BINDING SITE FOR RESIDUE CA A 900
09AC9SOFTWAREGLY A:73 , THR A:74 , HOH A:2130 , HOH A:2131 , HOH A:2132BINDING SITE FOR RESIDUE SO4 A 902
10BC1SOFTWAREILE A:56 , HIS A:58 , HOH A:2133 , HOH A:2134 , HOH A:2135 , ARG C:48 , LYS D:41 , HOH D:2046BINDING SITE FOR RESIDUE SO4 A 903
11BC2SOFTWARETYR B:36 , ASP B:100 , THR B:104 , ASN B:107 , ASN B:108 , GLA B:901 , GAL B:902BINDING SITE FOR RESIDUE CA B 900
12BC3SOFTWARELYS A:41 , ARG B:48 , HOH B:2102 , HOH B:2103 , HOH B:2104BINDING SITE FOR RESIDUE SO4 B 904
13BC4SOFTWARETYR C:36 , ASP C:100 , THR C:104 , ASN C:107 , ASN C:108 , GLA C:901 , GAL C:902BINDING SITE FOR RESIDUE CA C 900
14BC5SOFTWARETYR D:36 , ASP D:100 , THR D:104 , ASN D:107 , ASN D:108 , GLA D:901 , GAL D:902BINDING SITE FOR RESIDUE CA D 900
15BC6SOFTWAREASN A:88 , HOH A:2136 , HOH A:2137 , GLN C:45 , ASN C:78 , TRP D:33BINDING SITE FOR RESIDUE MPD A 905

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OKO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OKO)

(-) Exons   (0, 0)

(no "Exon" information available for 1OKO)

(-) 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:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d1okoa_ A: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains 1okoA00 A:1-121 Galactose-binding lectin                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oko A   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d1okob_ B: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains 1okoB00 B:1-121 Galactose-binding lectin                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee....eeeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oko B   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d1okoc_ C: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains 1okoC00 C:1-121 Galactose-binding lectin                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oko C   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with PA1L_PSEAE | Q05097 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           PA1L_PSEAE     2 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 122
               SCOP domains d1okod_ D: PA-IL, galactose-binding lectin 1                                                                              SCOP domains
               CATH domains 1okoD00 D:1-121 Galactose-binding lectin                                                                                  CATH domains
           Pfam domains (1) PA-IL-1okoD01 D:1-120                                                                                                   - Pfam domains (1)
           Pfam domains (2) PA-IL-1okoD02 D:1-120                                                                                                   - Pfam domains (2)
           Pfam domains (3) PA-IL-1okoD03 D:1-120                                                                                                   - Pfam domains (3)
           Pfam domains (4) PA-IL-1okoD04 D:1-120                                                                                                   - Pfam domains (4)
         Sec.struct. author .eeeeee......eeeeeee....eeeeeeeeeee.............................eeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oko D   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLICHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PA1L_PSEAE | Q05097)
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.
biological process
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1oko
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  PA1L_PSEAE | Q05097
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 Related Entries

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

UniProtKB/Swiss-Prot
        PA1L_PSEAE | Q05097: 1l7l 1uoj 2vxj 2wyf 3zyb 3zyf 3zyh 4a6s 4al9 4cp9 4cpb 4ljh 4lk6 4lk7 4lkd 4lke 4lkf 4yw6 4yw7 4ywa 5d21

(-) Related Entries Specified in the PDB File

1l7l CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1DETERMINED BY SINGLE WAVELENGTH ANOMALOUS SCATTERING PHASING METHOD
1uoj CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN 1 IN THE CALCIUM-FREE STATE