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(-) Description

Title :  CRYSTAL STRUCTURE OF LECA LECTIN COMPLEXED WITH A DIVALENT GALACTOSIDE AT 1.65 ANGSTROM
 
Authors :  J. Topin, A. Varrot, A. Imberty, N. Wissinger
Date :  04 Feb 14  (Deposition) - 08 Oct 14  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Sugar Binding Protein, Galactose Binding, Sugar Based Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Novoa, T. Eierhoff, J. Topin, A. Varrot, S. Barluenga, A. Imberty, W. Romer, N. Winssinger
A Leca Ligand Identified From A Galactoside-Conjugate Array Inhibits Host Cell Invasion By Pseudomonas Aeruginosa.
Angew. Chem. Int. Ed. Engl. V. 53 8885 2014
PubMed-ID: 25044671  |  Reference-DOI: 10.1002/ANIE.201402831

(-) Compounds

Molecule 1 - PA-I GALACTOPHILIC LECTIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25B
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Other Details: OXIDATED CYS57
    Strain: PAO1
    Synonym: PA-IL, GALACTOSE-BINDING LECTIN, LECA
 
Molecule 2 - PA-I GALACTOPHILIC LECTIN
    Chains: B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET25B
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Other Details: OXIDATED CYS57
    Strain: PAO1
    Synonym: PA-IL, GALACTOSE-BINDING LECTIN, LECA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 25)

Asymmetric Unit (8, 25)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2CA4Ligand/IonCALCIUM ION
3CN84Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO2Ligand/Ion1,2-ETHANEDIOL
5GAL4Ligand/IonBETA-D-GALACTOSE
6OCS4Mod. Amino AcidCYSTEINESULFONIC ACID
7SO42Ligand/IonSULFATE ION
8TRO1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN
Biological Unit 1 (7, 21)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3CN84Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO2Ligand/Ion1,2-ETHANEDIOL
5GAL4Ligand/IonBETA-D-GALACTOSE
6OCS4Mod. Amino AcidCYSTEINESULFONIC ACID
7SO42Ligand/IonSULFATE ION
8TRO1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN
Biological Unit 2 (6, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3CN81Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7SO41Ligand/IonSULFATE ION
8TRO1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN
Biological Unit 3 (5, 6)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3CN81Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO2Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7SO4-1Ligand/IonSULFATE ION
8TRO-1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN
Biological Unit 4 (4, 4)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3CN81Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7SO4-1Ligand/IonSULFATE ION
8TRO-1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN
Biological Unit 5 (5, 5)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA-1Ligand/IonCALCIUM ION
3CN81Ligand/Ion(4S)-N-ETHYL-4-{[N-METHYL-3-(1-{2-[(4-SULFANYLBENZOYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOL-4-YL)-L-ALANYL]AMINO}-L-PROLINAMIDE
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7SO41Ligand/IonSULFATE ION
8TRO-1Mod. Amino Acid2-HYDROXY-TRYPTOPHAN

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:36 , ASP A:100 , THR A:104 , ASN A:107 , ASN A:108 , GAL A:1123BINDING SITE FOR RESIDUE CA A1122
02AC2SOFTWAREALA A:12 , LYS A:68 , ILE A:97 , HOH A:2089 , 1PE B:1126BINDING SITE FOR RESIDUE 1PE A1125
03AC3SOFTWAREPRO A:38 , THR A:39 , GLN A:40 , HOH A:2069 , HOH A:2131 , THR D:104 , ASN D:107 , GAL D:1124 , HOH D:2088BINDING SITE FOR RESIDUE SO4 A1126
04AC4SOFTWARETYR B:36 , ASP B:100 , THR B:104 , ASN B:107 , ASN B:108 , GAL B:1124BINDING SITE FOR RESIDUE CA B1123
05AC5SOFTWARE1PE A:1125 , GLU B:11 , ALA B:12 , LYS B:68 , HOH B:2076BINDING SITE FOR RESIDUE 1PE B1126
06AC6SOFTWAREPHE B:61BINDING SITE FOR RESIDUE EDO B1127
07AC7SOFTWAREASP B:52 , HIS B:58BINDING SITE FOR RESIDUE EDO B1128
08AC8SOFTWARETYR C:36 , ASP C:100 , THR C:104 , ASN C:107 , ASN C:108 , GAL C:1124BINDING SITE FOR RESIDUE CA C1123
09AC9SOFTWAREALA C:12 , LYS C:68 , ILE C:97BINDING SITE FOR RESIDUE 1PE C1126
10BC1SOFTWARETYR D:36 , ASP D:100 , THR D:104 , ASN D:107 , ASN D:108 , GAL D:1124BINDING SITE FOR RESIDUE CA D1123
11BC2SOFTWARETHR A:104 , ASN A:107 , GAL A:1123 , PRO D:38 , THR D:39 , GLN D:40 , CN8 D:1125 , HOH D:2089 , HOH D:2090BINDING SITE FOR RESIDUE SO4 D1126
12BC3SOFTWAREALA D:12 , LYS D:68 , ASN D:71 , SER D:72 , HOH D:2075BINDING SITE FOR RESIDUE 1PE D1127
13BC4SOFTWARETYR A:36 , GLU A:49 , HIS A:50 , GLN A:53 , ASP A:100 , THR A:104 , ASN A:107 , CA A:1122 , HOH A:2065 , HOH A:2084 , HOH A:2128 , PRO D:38 , CN8 D:1125 , SO4 D:1126 , HOH D:2089BINDING SITE FOR POLY-SACCHARIDE RESIDUES GAL A1123 THROUGH CN8 A1124
14BC5SOFTWARETYR B:36 , GLU B:49 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:1123 , HOH B:2061 , HOH B:2075 , HOH B:2108 , GAL C:1124BINDING SITE FOR POLY-SACCHARIDE RESIDUES GAL B1124 THROUGH CN8 B1125
15BC6SOFTWARECN8 B:1125 , TYR C:36 , HIS C:50 , PRO C:51 , GLN C:53 , ASP C:100 , THR C:104 , ASN C:107 , CA C:1123 , HOH C:2048 , HOH C:2075BINDING SITE FOR POLY-SACCHARIDE RESIDUES GAL C1124 THROUGH CN8 C1125
16BC7SOFTWARECN8 A:1124 , SO4 A:1126 , TYR D:36 , GLN D:40 , GLU D:49 , HIS D:50 , PRO D:51 , GLN D:53 , ASP D:100 , THR D:104 , ASN D:107 , CA D:1123 , SO4 D:1126 , HOH D:2041 , HOH D:2042 , HOH D:2053 , HOH D:2088BINDING SITE FOR POLY-SACCHARIDE RESIDUES GAL D1124 THROUGH CN8 D1125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CP9)

(-) Exons   (0, 0)

(no "Exon" information available for 4CP9)

(-) 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: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 ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- 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
                 4cp9 A   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGwASYGPTQKWGPQGDREHPDQGLIcHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30  |     40        50      | 60        70        80        90       100       110       120 
                                                           33-TRO                  57-OCS                                                            


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 ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- 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
                 4cp9 B   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLIcHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50      | 60        70        80        90       100       110       120 
                                                                                   57-OCS                                                            


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 ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- 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
                 4cp9 C   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLIcHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50      | 60        70        80        90       100       110       120 
                                                                                   57-OCS                                                            


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 ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeeee.....eeeeeeeeee.........eee..............eeeeeeee.....ee...eeeee.......eeeeeee.....hhhhheeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cp9 D   1 AWKGEVLANNEAGQVTSIIYNPGDVITIVAAGWASYGPTQKWGPQGDREHPDQGLIcHDAFCGALVMKIGNSGTIPVNTGLFRWVAPNNVQGAITLIYNDVPGTYGNNSGSFSVNIGKDQS 121
                                    10        20        30        40        50      | 60        70        80        90       100       110       120 
                                                                                   57-OCS
   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  (0, 0)

(no "SCOP Domain" information available for 4CP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CP9)

(-) Gene Ontology  (5, 5)

Asymmetric 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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  PA1L_PSEAE | Q05097
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  PA1L_PSEAE | Q05097
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4cpb CRYSTAL STRUCTURE OF LECA IN COMPLEX WITH A DIVALENT GALACTOSIDE AT 1.57 ANGSTROM IN MAGNESIUM