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(-) Description

Title :  DISCOVERY OF GLYCOMIMETIC LIGANDS VIA GENETICALLY-ENCODED LIBRARY OF PHAGE DISPLAYING MANNOSE-PEPTIDES
 
Authors :  S. Ng, E. Lin, K. F. Tjhung, O. Gerlits, A. Sood, B. Kasper, L. Deng, P. I. K W. L. Matochko, B. M. Paschal, C. J. Noren, J. Klassen, L. K. Mahal, L. Co R. J. Woods, R. Derda
Date :  22 Apr 14  (Deposition) - 22 Apr 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ng, E. Lin, P. I. Kitov, K. F. Tjhung, O. O. Gerlits, L. Deng, B. Kasper A. Sood, B. M. Paschal, P. Zhang, C. C. Ling, J. S. Klassen, C. J. Noren, L. K. Mahal, R. J. Woods, L. Coates, R. Derda
Genetically-Encoded Fragment-Based Discovery Of Glycopeptide Ligands For Carbohydrate-Binding Proteins.
J. Am. Chem. Soc. V. 137 5248 2015
PubMed-ID: 25860443  |  Reference-DOI: 10.1021/JA511237N

(-) Compounds

Molecule 1 - CONCANAVALIN-A
    Chains: A, B, C, D
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA CATHARTICA
    Organism Taxid: 28958
    Synonym: CON A, CONCANAVALIN A
 
Molecule 2 - MAN-WYD
    Chains: E, F, G, H
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
18LR4Mod. Amino Acid2-HYDROXYETHYL ALPHA-D-MANNOPYRANOSIDE
2CA4Ligand/IonCALCIUM ION
3MN4Ligand/IonMANGANESE (II) ION
4XSN4Mod. Amino AcidL-ALPHA-ASPARAGINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:2020 , HOH A:2021BINDING SITE FOR RESIDUE CA A1239
2AC2SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:2017 , HOH B:2018BINDING SITE FOR RESIDUE CA B1239
3AC3SOFTWAREASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:2018 , HOH C:2019BINDING SITE FOR RESIDUE CA C1239
4AC4SOFTWAREASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:2022 , HOH D:2023BINDING SITE FOR RESIDUE CA D1239
5AC5SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:2017 , HOH A:2018BINDING SITE FOR RESIDUE MN A1240
6AC6SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:2014 , HOH B:2015BINDING SITE FOR RESIDUE MN B1240
7AC7SOFTWAREGLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:2015 , HOH C:2016BINDING SITE FOR RESIDUE MN C1240
8AC8SOFTWAREGLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:2020 , HOH D:2021BINDING SITE FOR RESIDUE MN D1240

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:207 -Asp A:208
2Ala B:207 -Asp B:208
3Ala C:207 -Asp C:208
4Ala D:207 -Asp D:208
5Tyr G:4 -Xsn G:5
6Tyr H:4 -Xsn H:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CZS)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4czs A   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4czs B   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4czs C   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee.....eeeeeeee.........eeeee..ee.hhh.ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4czs D   1 ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4czs E   1 xGWYn   5
                            |   |
                            1-8LR
                                5-XSN


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4czs F   1 xGWYn   5
                            |   |
                            |   |
                            1-8LR
                                5-XSN


Chain G from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4czs G   1 xGWYn   5
                            |   |
                            |   |
                            1-8LR
                                5-XSN


Chain H from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4czs H   1 xGWYn   5
                            |   |
                            |   |
                            1-8LR
                                5-XSN
   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 4CZS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:207 - Asp A:208   [ RasMol ]  
    Ala B:207 - Asp B:208   [ RasMol ]  
    Ala C:207 - Asp C:208   [ RasMol ]  
    Ala D:207 - Asp D:208   [ RasMol ]  
    Tyr G:4 - Xsn G:5   [ RasMol ]  
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        CONA_CANCT | P81461: 1hqw 1qgl 2a7a 2g4i 3qlq 5f5q

(-) Related Entries Specified in the PDB File

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