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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE ANTI- METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS (MRSA) ACTIVITY OF CEFTOBIPROLE
 
Authors :  A. L. Lovering, M. C. Gretes, N. C. J. Strynadka
Date :  03 Feb 12  (Deposition) - 01 Aug 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Enzyme, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Lovering, M. C. Gretes, S. S. Safadi, F. Danel, L. De Castro, M. G. Page, N. C. Strynadka
Structural Insights Into The Anti-Methicillin-Resistant Staphylococcus Aureus (Mrsa) Activity Of Ceftobiprole.
J. Biol. Chem. V. 287 32096 2012
PubMed-ID: 22815485  |  Reference-DOI: 10.1074/JBC.M112.355644

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2'
    Chains: A, B
    EC Number: 3.4.16.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 24-668
    Gene: MECA, SACOL0033
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1BCT4Ligand/IonBICARBONATE ION
2CD7Ligand/IonCADMIUM ION
3CL4Ligand/IonCHLORIDE ION
4RB62Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(5-AMINO-1,2,4-THIADIAZOL-3-YL)-2-(HYDROXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-({2-OXO-1-[(3R)-PYRROLIDIN-3-YL]-2,5-DIHYDRO-1H-PYRROL-3-YL}METHYL)-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLICACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BCT3Ligand/IonBICARBONATE ION
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
4RB61Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(5-AMINO-1,2,4-THIADIAZOL-3-YL)-2-(HYDROXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-({2-OXO-1-[(3R)-PYRROLIDIN-3-YL]-2,5-DIHYDRO-1H-PYRROL-3-YL}METHYL)-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLICACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
4RB61Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(5-AMINO-1,2,4-THIADIAZOL-3-YL)-2-(HYDROXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-({2-OXO-1-[(3R)-PYRROLIDIN-3-YL]-2,5-DIHYDRO-1H-PYRROL-3-YL}METHYL)-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLICACID
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1BCT4Ligand/IonBICARBONATE ION
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
4RB62Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(5-AMINO-1,2,4-THIADIAZOL-3-YL)-2-(HYDROXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-({2-OXO-1-[(3R)-PYRROLIDIN-3-YL]-2,5-DIHYDRO-1H-PYRROL-3-YL}METHYL)-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLICACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:403 , LYS A:406 , TYR A:446 , SER A:462 , ASN A:464 , GLY A:520 , GLN A:521 , SER A:598 , GLY A:599 , THR A:600 , ALA A:601 , GLU A:602 , MET A:641 , ALA A:642 , HOH A:806BINDING SITE FOR RESIDUE RB6 A 701
02AC2SOFTWAREARG A:151 , THR A:165 , ARG A:241 , VAL A:277BINDING SITE FOR RESIDUE BCT A 702
03AC3SOFTWAREASP A:128 , HIS A:129 , GLN A:137 , LYS A:138BINDING SITE FOR RESIDUE BCT A 703
04AC4SOFTWARELYS A:153 , ASP A:323 , LYS B:153 , ASP B:323BINDING SITE FOR RESIDUE BCT A 704
05AC5SOFTWAREHIS A:143 , GLU A:145 , CL A:708 , GLU B:145BINDING SITE FOR RESIDUE CD A 705
06AC6SOFTWAREHIS A:232BINDING SITE FOR RESIDUE CD A 706
07AC7SOFTWAREGLY A:135 , HIS A:311 , CL A:709 , ASP B:209BINDING SITE FOR RESIDUE CD A 707
08AC8SOFTWAREGLU A:145 , THR A:300 , CD A:705 , GLU B:145BINDING SITE FOR RESIDUE CL A 708
09AC9SOFTWAREGLN A:137 , GLN A:140 , CD A:707 , GLN B:207 , ASP B:209BINDING SITE FOR RESIDUE CL A 709
10BC1SOFTWARESER B:403 , LYS B:406 , TYR B:446 , SER B:462 , ASN B:464 , TYR B:519 , GLY B:520 , GLN B:521 , SER B:598 , GLY B:599 , THR B:600 , GLU B:602 , ALA B:642BINDING SITE FOR RESIDUE RB6 B 701
11BC2SOFTWAREASP B:35 , GLU B:38BINDING SITE FOR RESIDUE BCT B 702
12BC3SOFTWAREGLU A:145 , HIS B:143 , GLU B:145 , ASN B:307 , CL B:707BINDING SITE FOR RESIDUE CD B 703
13BC4SOFTWAREASP A:209 , GLY B:135 , HIS B:311 , CL B:708BINDING SITE FOR RESIDUE CD B 704
14BC5SOFTWAREGLU A:59 , HIS B:232BINDING SITE FOR RESIDUE CD B 705
15BC6SOFTWARELYS A:434 , ASN B:569 , ASP B:573BINDING SITE FOR RESIDUE CD B 706
16BC7SOFTWAREGLU A:145 , GLU B:145 , ARG B:298 , THR B:300 , CD B:703BINDING SITE FOR RESIDUE CL B 707
17BC8SOFTWAREGLN A:207 , GLY B:135 , GLN B:137 , GLN B:140 , HIS B:311 , CD B:704BINDING SITE FOR RESIDUE CL B 708

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:363 -Pro A:364
2Thr B:363 -Pro B:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DKI)

(-) 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:641
 aligned with A0A0H2WXF8_S | A0A0H2WXF8 from UniProtKB/TrEMBL  Length:668

    Alignment length:644
                                    34        44        54        64        74        84        94       104       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    
         A0A0H2WXF8_S    25 SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d4dkia1 A:25-138 Penicillin binding protein 2a (PBP2A), N-terminal domain                                         d4dkia2 A:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d4dkia3 A:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..eeeee.hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhh.........eeeeee...hhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhheeee.hhhhhhh..........eeeeehhhhhhhhhhh...eeeeeeee.....eeeeeeee.......ee...hhhhhhhhhhh....eeeeeee......eeeeeee....hhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......................hhhhhhhhhh.......hhhhhhhhhhh......ee...........eee....hhhhhhhhhhhhhhhhhh.hhhhhh.....eeeeee........-.....eeeeeeee......eeeeeee....--.hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dki A  25 SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQ-ETGRQIGWFISYDKDNPNMMMAINVKDVQD--MASYNAKISGKVYDELYENGNKKYDIDE 668
                                    34        44        54        64        74        84        94       104       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    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                607 |                          638  |                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  609                             641                           


Chain B from PDB  Type:PROTEIN  Length:632
 aligned with A0A0H2WXF8_S | A0A0H2WXF8 from UniProtKB/TrEMBL  Length:668

    Alignment length:644
                                    34        44        54        64        74        84        94       104       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    
         A0A0H2WXF8_S    25 SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 668
               SCOP domains d4dkib1 B:25-138 Penicillin binding protein 2a (PBP2A), N-terminal domain                                         d4dkib2 B:139-327 Penicillin binding protein 2a (PBP2A), middle domain                                                                                                                       d4dkib3 B:328-668 Penicillin binding protein 2a (PBP2A), C-terminal domain                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeee..eeeee.hhhhh.......eeeeeeee......ee.....eeeeeeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhh.........eeeeee...hhhhhhhhh....eeeeeeeee..hhhhhhhhhheeee...hhhhh..........eeeeehhhhhhhhhhh...eeeeeeee....eeeeeeeee.......ee...hhhhhhhhhhh....eeeeeee......eeeeeee.....hhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhh.......eeee...ee..hhhhh...ee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................-....hhhhhhhhh........hhhhhhhhhhhhhh...ee...........eee....hhhhhhhhhhhhhhhhhh.hhhhhh.....eeeeeee....-------...eeeeeee..eeeeeeeeeee..----.hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dki B  25 SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQIS-KNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELK-------RQIGWFISYDKDNPNMMMAINVKDV----MASYNAKISGKVYDELYENGNKKYDIDE 668
                                    34        44        54        64        74        84        94       104       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    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         504 |                                                                                               604     612                     636  641                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           506
   Legend:   → Mismatch (orange background)
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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  (3, 6)

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 4DKI)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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