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(-) Description

Title :  X-RAY STRUCTURE OF A LECTIN-BOUND DNA DUPLEX CONTAINING AN UNNATURAL PHENANTHRENYL PAIR
 
Authors :  P. Roethlisberger, A. Istrate, M. J. Marcaida Lopez, R. Visini, A. Sto C. J. Leumann
Date :  04 Jan 16  (Deposition) - 02 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,E
Biol. Unit 1:  A,B,E  (4x)
Keywords :  Lecb, Complex, Artificial Dna, Phenanthrene, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Roethlisberger, A. Istrate, M. J. Marcaida Lopez, R. Visini, A. Stocker, J. L. Reymond, C. J. Leumann
X-Ray Structure Of A Lectin-Bound Dna Duplex Containing An Unnatural Phenanthrenyl Pair.
Chem. Commun. (Camb. ) V. 52 4749 2016
PubMed-ID: 26898721  |  Reference-DOI: 10.1039/C6CC00374E

(-) Compounds

Molecule 1 - FUCOSE-BINDING LECTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLECB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ERS445055_01627, PA8380_17510, PAERUG_E15_LONDON_28_01_14_00983, PAERUG_P32_LONDON_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    SynonymFUCOSE-BINDING LECTIN II (PA-IIL),FUCOSE-BINDING LECTIN PA- IIL,PHOTOPEXIN A
 
Molecule 2 - DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3')
    ChainsE
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABE
Biological Unit 1 (4x)ABE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
161H2Mod. Nucleotide(1R)-1,4-ANHYDRO-2-DEOXY-5-O-[(S)-HYDROXY(OXIDO)-LAMBDA~5~-PHOSPHANYL]-1-PHENANTHREN-2-YL-D-ERYTHRO-PENTITOL
261J1Ligand/Ion(6S)-2,6-ANHYDRO-1-DEOXY-6-(2-{[(S)-HYDROXY(OXIDO)-LAMBDA~5~-PHOSPHANYL]OXY}ETHYL)-D-GALACTITOL
3CA2Ligand/IonCALCIUM ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
161H8Mod. Nucleotide(1R)-1,4-ANHYDRO-2-DEOXY-5-O-[(S)-HYDROXY(OXIDO)-LAMBDA~5~-PHOSPHANYL]-1-PHENANTHREN-2-YL-D-ERYTHRO-PENTITOL
261J4Ligand/Ion(6S)-2,6-ANHYDRO-1-DEOXY-6-(2-{[(S)-HYDROXY(OXIDO)-LAMBDA~5~-PHOSPHANYL]OXY}ETHYL)-D-GALACTITOL
3CA-1Ligand/IonCALCIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , 61J E:101binding site for residue CA A 201
2AC2SOFTWAREASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , 61J E:101binding site for residue CA A 202
3AC3SOFTWAREASN A:21 , SER A:22 , SER A:23 , GLU A:95 , ASP A:96 , GLY A:97 , ASP A:99 , ASP A:101 , ASP A:104 , CA A:201 , CA A:202 , DC B:13 , DG E:14binding site for residue 61J E 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HCH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:111 -Pro A:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HCH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HCH)

(-) Exons   (0, 0)

(no "Exon" information available for 5HCH)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee..ee.eeeeeeeee...eeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5hch A   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110    

Chain B from PDB  Type:DNA  Length:13
                                             
                 5hch B   1 CGCATTxTATCGC  13
                                  | 10   
                                  7-61H  

Chain E from PDB  Type:DNA  Length:13
                                             
                 5hch E  14 GCGATAxAATGCG  26
                                  | 23   
                                 20-61H  

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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 5HCH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HCH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HCH)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9HYN5_PSEAE | Q9HYN51gzt 1our 1ous 1oux 1ovp 1ovs 1oxc 1uzv 1w8f 1w8h 2boj 2bp6 2jdh 2jdk 2jdm 2jdn 2jdp 2jdu 2jdy 2vuc 2vud 3dcq 3zdv 4ce8 5a3o 5d2a

(-) Related Entries Specified in the PDB File

1oxc 1OXC CONTAINS THE SAME PROTEIN COMPLEXED TO FUCOSE