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(-) Description

Title :  CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH ATROPINE BY CO-CRYSTALLIZATION
 
Authors :  N. Silva-Martin, J. A. Hermoso
Date :  10 Mar 10  (Deposition) - 06 Apr 11  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A
Keywords :  Choline-Binding Protein, Lipid-Binding-Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. S. Martin, M. G. Retamosa, B. Maestro, S. G. Bartual, M. J. Rodes, P. Garcia, J. M. Sanz, J. A. Hermoso
Crystal Structures Of Cbpf Complexed With Atropine And Ipratropium Reveal Clues For The Design Of Novel Antimicrobials Against Streptococcus Pneumoniae.
Biochim. Biophys. Acta V. 1840 129 2013
PubMed-ID: 24036328  |  Reference-DOI: 10.1016/J.BBAGEN.2013.09.006

(-) Compounds

Molecule 1 - CHOLINE-BINDING PROTEIN F
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIN-III-A3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 28-338
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1CHT5Ligand/IonCHOLINE ION
2GOL2Ligand/IonGLYCEROL
3OIN2Ligand/Ion(1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL(2R)-3-HYDROXY-2-PHENYLPROPANOATE
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:244 , ARG A:246 , SER A:247 , HOH A:2270BINDING SITE FOR RESIDUE SO4 A1312
02AC2SOFTWARETRP A:194 , LYS A:196 , TRP A:201 , SER A:248 , HOH A:2001 , HOH A:2038 , HOH A:2268 , HOH A:2274BINDING SITE FOR RESIDUE OIN A1313
03AC3SOFTWARETYR A:203 , SER A:206 , LYS A:215 , HOH A:2272BINDING SITE FOR RESIDUE GOL A1314
04AC4SOFTWARETRP A:163 , TRP A:181 , LYS A:227 , ASN A:228 , HOH A:2169BINDING SITE FOR RESIDUE OIN A1315
05AC5SOFTWARETYR A:48 , GLN A:72 , GLU A:73 , LEU A:143 , TYR A:151 , ILE A:156 , THR A:170 , HOH A:2273BINDING SITE FOR RESIDUE GOL A1316
06AC6SOFTWARETRP A:283 , TYR A:301 , TRP A:309BINDING SITE FOR RESIDUE CHT A1317
07AC7SOFTWAREHOH A:2274BINDING SITE FOR RESIDUE CHT A1318
08AC8SOFTWARETRP A:235 , TRP A:242 , SER A:289BINDING SITE FOR RESIDUE CHT A1319
09AC9SOFTWARETRP A:214 , TRP A:221 , ASN A:269 , HOH A:2230BINDING SITE FOR RESIDUE CHT A1320
10BC1SOFTWARETRP A:130 , TRP A:137 , TYR A:182 , MET A:190 , SER A:207BINDING SITE FOR RESIDUE CHT A1321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X8P)

(-) Exons   (0, 0)

(no "Exon" information available for 2X8P)

(-) 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:311
 aligned with Q8DR52_STRR6 | Q8DR52 from UniProtKB/TrEMBL  Length:338

    Alignment length:311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q8DR52_STRR6    28 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDFHVTIDIDRSKPAPWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 338
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (8)
           Pfam domains (9) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2x8pA0------------------- Pfam domains (9)
         Sec.struct. author ....eeeeee..eeeeee..eeee.eeee..eeee.........eeeeee.........ee...........eeeeee...........eeeee....................eeeee.........eeeee..eeeee....ee....ee.........eeee...............eeee.........eeee..eeee.........eeeee..eeeee.........eeee....eeee........eeeee..eeeee.........eeeee..eeeee.........eee..eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8p A   1 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDFHVTIDIDRSKPAPWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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 2X8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X8P)

(-) Pfam Domains  (1, 9)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CW_binding_1] (12)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2X8P)

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 Related Entries

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UniProtKB/TrEMBL
        Q8DR52_STRR6 | Q8DR52: 2v04 2v05 2vyu 2x8m 2x8o

(-) Related Entries Specified in the PDB File

2v04 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE
2v05 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE. CRYSTAL FORM II.
2vyu CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE IN THE PRESENCE OF A PEPTIDOGLYCAN ANALOGUE ( TETRASACCHARIDE-PENTAPEPTIDE)
2x8m CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH IPRATROPIUM BY SOAKING
2x8o CRYSTAL STRUCTURE OF CBPF IN COMPLEX WITH ATROPINE BY SOAKING