Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA3)
 
Authors :  C. Contreras-Martel, A. Amoroso, E. C. Woon, A. Zervosen, S. Inglis, A. O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. J. Schofield, A. D
Date :  15 Dec 10  (Deposition) - 03 Aug 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Infection, Cell Wall, Peptidoglycan, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contreras-Martel, A. Amoroso, E. C. Woon, A. Zervosen, S. Inglis, A. Martins, O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. J. Schofield, A. Dessen
Structure-Guided Design Of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance In Staphylococcus Aureus (Mrsa).
Acs Chem. Biol. V. 6 943 2011
PubMed-ID: 21732689  |  Reference-DOI: 10.1021/CB2001846

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
    Chains: A
    EC Number: 2.4.1.129, 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) PLYS
    Expression System Taxid: 469008
    Expression System Vector: PGEX
    Expression System Vector Type: PLASMID
    Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Other Details: ALKYL BORONATE (ZA3) COVALENTLY BOND TO S460
    Strain: R6
    Synonym: PBP1B

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CL11Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION
4ZA31Ligand/IonTRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION
4ZA32Ligand/IonTRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:459 , SER A:460 , LYS A:463 , ASN A:492 , SER A:516 , ASN A:518 , SER A:553 , MET A:556 , GLY A:557 , GLY A:558 , GLY A:653 , THR A:654 , NA A:1300BINDING SITE FOR RESIDUE ZA3 A1000
02AC2SOFTWARETHR A:563 , LYS A:583 , HOH A:2102 , HOH A:2111 , HOH A:2351 , HOH A:2352 , HOH A:2353 , HOH A:2354BINDING SITE FOR RESIDUE SO4 A1100
03AC3SOFTWAREARG A:529 , HOH A:2186BINDING SITE FOR RESIDUE CL A1200
04AC4SOFTWAREVAL A:535 , LYS A:536 , HOH A:2164BINDING SITE FOR RESIDUE CL A1201
05AC5SOFTWAREARG A:627 , LYS A:633BINDING SITE FOR RESIDUE CL A1202
06AC6SOFTWAREASN A:759 , LYS A:760 , SER A:761BINDING SITE FOR RESIDUE CL A1203
07AC7SOFTWAREALA A:592 , ASP A:593 , ARG A:595BINDING SITE FOR RESIDUE CL A1206
08AC8SOFTWARESER A:726 , GLU A:727 , LYS A:735BINDING SITE FOR RESIDUE CL A1208
09AC9SOFTWARETYR A:544 , GLU A:545 , HOH A:2194 , HOH A:2351BINDING SITE FOR RESIDUE CL A1211
10BC1SOFTWAREGLU A:346 , HIS A:584 , VAL A:585 , ILE A:586BINDING SITE FOR RESIDUE CL A1212
11BC2SOFTWAREASP A:337 , TYR A:338 , LEU A:339 , HIS A:399 , GLN A:403BINDING SITE FOR RESIDUE CL A1213
12BC3SOFTWARETHR A:652 , THR A:654 , ZA3 A:1000BINDING SITE FOR RESIDUE NA A1300
13BC4SOFTWARESER A:634BINDING SITE FOR RESIDUE CL A1791
14BC5SOFTWAREASN A:492 , ASN A:494BINDING SITE FOR RESIDUE CL A1792

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y2I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y2I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y2I)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y2I)

(-) 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:467
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:684
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784    
         Q7CRA4_STRR6   105 ISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVG 788
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.....eeee.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee...................hhhhhhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeee.....eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee.......eeee....eeee...eeeeee.................hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y2i A 105 ISEITYSDGTVIASI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVG 788
                                   114    |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |    344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784    
                                        119                                                                                                                                                                                                                       337
   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 2Y2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y2I)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7CRA4_STRR6 | Q7CRA4)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
    GO:0008955    peptidoglycan glycosyltransferase activity    Catalysis of the reaction: [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-diphosphoundecaprenol + GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZA3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y2i)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2y2i
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q7CRA4_STRR6 | Q7CRA4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.4.1.129
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q7CRA4_STRR6 | Q7CRA4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7CRA4_STRR6 | Q7CRA4: 2uwx 2xd1 2xd5 2y2g 2y2h 2y2j 2y2k 2y2l 2y2m 2y2n 2y2o 2y2p 2y2q

(-) Related Entries Specified in the PDB File

2uwx ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd1 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd5 STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF STREPTOCOCCUS PNEUMONIAE PBP1B
2y2g PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (A01)
2y2h PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA2)
2y2j PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA4)
2y2k PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)
2y2l PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E06)
2y2m PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E08)
2y2n PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E07)
2y2o PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (EO9)
2y2p PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z10)
2y2q PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z06)