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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL INSIGHT INTO THE TRANSGLYCOSYLATION STEP OF BACTERIAL CELL WALL BIOSYNTHESIS : DONOR LIGAND COMPLEX
 
Authors :  A. L. Lovering, L. De Castro, D. Lim, N. C. J. Strynadka
Date :  19 Jan 07  (Deposition) - 13 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transpeptidase Fold, Glycosyltransferase Family 51, Lysozyme Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Lovering, L. H. De Castro, D. Lim, N. C. Strynadka
Structural Insight Into The Transglycosylation Step Of Bacterial Cell-Wall Biosynthesis.
Science V. 315 1402 2007
PubMed-ID: 17347437  |  Reference-DOI: 10.1126/SCIENCE.1136611

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2
    Chains: A, B
    EC Number: 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A
    Expression System Strain: ROSETTA LAMBDA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PBP2
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1M0E2Ligand/IonMOENOMYCIN
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1M0E1Ligand/IonMOENOMYCIN
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
1M0E1Ligand/IonMOENOMYCIN
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:114 , GLY A:145 , GLN A:152 , LYS A:155 , ASP A:156 , LYS A:163 , ARG A:167 , LYS A:168 , GLU A:171 , TYR A:196 , PRO A:231 , GLN A:232 , VAL A:233 , PRO A:234 , ASN A:235BINDING SITE FOR RESIDUE M0E A 901
2AC2SOFTWAREGLU B:114 , GLY B:145 , GLN B:152 , LYS B:155 , ASP B:156 , LYS B:163 , ARG B:167 , LYS B:168 , GLU B:171 , TYR B:196 , PRO B:231 , GLN B:232 , VAL B:233 , PRO B:234 , ASN B:235BINDING SITE FOR RESIDUE M0E B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:673 -Pro A:674
2Ile B:673 -Pro B:674

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OLV)

(-) 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:617
 aligned with Q9R744_STAAU | Q9R744 from UniProtKB/TrEMBL  Length:727

    Alignment length:626
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686      
         Q9R744_STAAU    67 AKLQDPIPAKIYDKNGELVKTLDNGQRHEHVNLKDVPKSMKDAVLATEDNRFYEHGALDYKRLFGAIGKNLTGGFGSEGASTLTQQVVKDAFLSQHKSIGRKAQEAYLSYRLEQEYSKDDIFQVYLNKIYYSDGVTGIKAAAKYYFNKDLKDLNLAEEAYLAGLPQVPNNYNIYDHPKAAEDRKNTVLYLMHYHKRITDKQWEDAKKIDLKANLVNRTPEERQNIDTNQDSEYNSYVNFVKSELMNNKAFKDENLGNVLQSGIKIYTNMDKDVQKTLQNDVDNGSFYKNKDQQVGATILDSKTGGLVAISGGRDFKDVVNRNQATDPHPTGSSLKPFLAYGPAIENMKWATNHAIQDESSYQVDGSTFRNYDTKSHGTVSIYDALRQSFNIPALKAWQSVKQNAGNDAPKKFAAKLGLNYEGDIGPSEVLGGSASEFSPTQLASAFAAIANGGTYNNAHSIQKVVTRDGETIEYDHTSHKAMSDYTAYMLAEMLKGTFKPYGSAYGHGVSGVNMGAKTGTGTYGAETYSQYNLPDNAAKDVWINGFTPQYTMSVWMGFSKVKQYGENSFVGHSQQEYPQFLYENVMSKISSRDGEDFKRPSSVSGSIPSINVSGSQDNNTTNRSTH 692
               SCOP domains d2olva1 A:67-292 Penicillin-binding protein 2, PBP2                                                                                                                                                                               d2olva2 A:293-692 Penicillin-binding protein 2, PBP2                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....eeee...............hhhhhhhhhhhhh..........hhhhhhhhh.---------...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhh....eeee..hhhhhhhhhhhhhhh.......eeeeeeeee.....eeeee.................ee.hhhhhhhhhhhhhhhhhh.....eee....ee....ee.........eeehhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhh.....eehhhhhhhhhhhhhh..eee....eeeee.....eee....eee..hhhhhhhhhhhhhhhh................eeeeeee..hhhhhhhh.....ee.eeeeeee...eeeeeeeee...hhhhh..eehhhhhhhhhhhhhhhhhhhh............eeee..eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olv A  67 AKLQDPIPAKIYDKNGELVKTLDNGQRHEHVNLKDVPKSmKDAVLATEDNRFYEHGALDYKRLFGAIGK---------GASTLTQQVVKDAFLSQHKSIGRKAQEAYLSYRLEQEYSKDDIFQVYLNKIYYSDGVTGIKAAAKYYFNKDLKDLNLAEEAYLAGLPQVPNNYNIYDHPKAAEDRKNTVLYLmHYHKRITDKQWEDAKKIDLKANLVNRTPEERQNIDTNQDSEYNSYVNFVKSELmNNKAFKDENLGNVLQSGIKIYTNmDKDVQKTLQNDVDNGSFYKNKDQQVGATILDSKTGGLVAISGGRDFKDVVNRNQATDPHPTGSSLKPFLAYGPAIENmKWATNHAIQDESSYQVDGSTFRNYDTKSHGTVSIYDALRQSFNIPALKAWQSVKQNAGNDAPKKFAAKLGLNYEGDIGPSEVLGGSASEFSPTQLASAFAAIANGGTYNNAHSIQKVVTRDGETIEYDHTSHKAmSDYTAYmLAEmLKGTFKPYGSAYGHGVSGVNmGAKTGTGTYGAETYSQYNLPDNAAKDVWINGFTPQYTmSVWmGFSKVKQYGENSFVGHSQQEYPQFLYENVmSKISSRDGEDFKRPSSVSGSIPSINVSGSQDNNTTNRSTH 692
                                    76        86        96       106       116       126        |-       146       156       166       176       186       196       206       216       226       236       246       256|      266       276       286       296       306    |  316       326       336       346       356       366       376       386       396       406      |416       426       436       446       456       466       476       486       496       506       516       526       536       546 |     556  |    566       576   |   586       596       606       616 |   | 626       636       646     | 656       666       676       686      
                                                                 106-MSE                      135       145                                                                                                             257-MSE                                               311-MSE                 335-MSE                                                                       413-MSE                                                                                                                                548-MSE  |   |                  580-MSE                               618-MSE                           652-MSE                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  555-MSE                                                            622-MSE                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      559-MSE                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:618
 aligned with Q9R744_STAAU | Q9R744 from UniProtKB/TrEMBL  Length:727

    Alignment length:626
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686      
         Q9R744_STAAU    67 AKLQDPIPAKIYDKNGELVKTLDNGQRHEHVNLKDVPKSMKDAVLATEDNRFYEHGALDYKRLFGAIGKNLTGGFGSEGASTLTQQVVKDAFLSQHKSIGRKAQEAYLSYRLEQEYSKDDIFQVYLNKIYYSDGVTGIKAAAKYYFNKDLKDLNLAEEAYLAGLPQVPNNYNIYDHPKAAEDRKNTVLYLMHYHKRITDKQWEDAKKIDLKANLVNRTPEERQNIDTNQDSEYNSYVNFVKSELMNNKAFKDENLGNVLQSGIKIYTNMDKDVQKTLQNDVDNGSFYKNKDQQVGATILDSKTGGLVAISGGRDFKDVVNRNQATDPHPTGSSLKPFLAYGPAIENMKWATNHAIQDESSYQVDGSTFRNYDTKSHGTVSIYDALRQSFNIPALKAWQSVKQNAGNDAPKKFAAKLGLNYEGDIGPSEVLGGSASEFSPTQLASAFAAIANGGTYNNAHSIQKVVTRDGETIEYDHTSHKAMSDYTAYMLAEMLKGTFKPYGSAYGHGVSGVNMGAKTGTGTYGAETYSQYNLPDNAAKDVWINGFTPQYTMSVWMGFSKVKQYGENSFVGHSQQEYPQFLYENVMSKISSRDGEDFKRPSSVSGSIPSINVSGSQDNNTTNRSTH 692
               SCOP domains d2olvb1 B:67-292 Penicillin-binding protein 2, PBP2                                                                                                                                                                               d2olvb2 B:293-692 Penicillin-binding protein 2, PBP2                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.....eeee..........hhhhhhhhhhhhhhhhhh..........hhhhhhhhh..--------...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........hhhhhh......hhhhhhhhhhhhhhhh........hhhhhhh...eeee..hhhhhhhhhhhhh.........eeeeeeeee.....eeeee.................ee.hhhhhhhhhhhhhhhhhh......ee....ee....ee.........eehhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhh.....eehhhhhhhhhhhhhh..eee....eeeee.....eee....eee..hhhhhhhhhhhhhhhhh...............eeeeeee..hhhhhhhh.....ee.eeeeeee...eeeeeeeee...hhhhh..eehhhhhhhhhhhhhhhhhhhh............eeee..eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olv B  67 AKLQDPIPAKIYDKNGELVKTLDNGQRHEHVNLKDVPKSmKDAVLATEDNRFYEHGALDYKRLFGAIGKN--------GASTLTQQVVKDAFLSQHKSIGRKAQEAYLSYRLEQEYSKDDIFQVYLNKIYYSDGVTGIKAAAKYYFNKDLKDLNLAEEAYLAGLPQVPNNYNIYDHPKAAEDRKNTVLYLmHYHKRITDKQWEDAKKIDLKANLVNRTPEERQNIDTNQDSEYNSYVNFVKSELmNNKAFKDENLGNVLQSGIKIYTNmDKDVQKTLQNDVDNGSFYKNKDQQVGATILDSKTGGLVAISGGRDFKDVVNRNQATDPHPTGSSLKPFLAYGPAIENmKWATNHAIQDESSYQVDGSTFRNYDTKSHGTVSIYDALRQSFNIPALKAWQSVKQNAGNDAPKKFAAKLGLNYEGDIGPSEVLGGSASEFSPTQLASAFAAIANGGTYNNAHSIQKVVTRDGETIEYDHTSHKAmSDYTAYmLAEmLKGTFKPYGSAYGHGVSGVNmGAKTGTGTYGAETYSQYNLPDNAAKDVWINGFTPQYTmSVWmGFSKVKQYGENSFVGHSQQEYPQFLYENVmSKISSRDGEDFKRPSSVSGSIPSINVSGSQDNNTTNRSTH 692
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256|      266       276       286       296       306    |  316       326       336       346       356       366       376       386       396       406      |416       426       436       446       456       466       476       486       496       506       516       526       536       546 |     556  |    566       576   |   586       596       606       616 |   | 626       636       646     | 656       666       676       686      
                                                                 106-MSE                       136      145                                                                                                             257-MSE                                               311-MSE                 335-MSE                                                                       413-MSE                                                                                                                                548-MSE  |   |                  580-MSE                               618-MSE                           652-MSE                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  555-MSE                                                            622-MSE                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      559-MSE
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9R744_STAAU | Q9R744)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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
    M0E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:673 - Pro A:674   [ RasMol ]  
    Ile B:673 - Pro B:674   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  2olv
    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
  Q9R744_STAAU | Q9R744
    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
 
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
  Q9R744_STAAU | Q9R744
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9R744_STAAU | Q9R744: 2olu

(-) Related Entries Specified in the PDB File

2olu STRUCTURAL INSIGHT INTO THE TRANSGLYCOSYLATION STEP OF BACTERIAL CELL WALL BIOSYNTHESIS: APOENZYME