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(-) Description

Title :  PENICILLIN-BINDING PROTEIN 2X (PBP 2X) ACYL-ENZYME COMPLEX (TEBIPENEM) FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  M. Yamada, T. Watanabe, Y. Takeuchi
Date :  02 Nov 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Peptidoglycan Synthesis, Cell Wall, Penicillin-Binding, Antibiotics, Tebipenem, Antibiotic Resistance, Cell Cycle, Cell Division, Cell Shape, Cell Wall Biogenesis/Degradation, Membrane, Secreted, Transmembrane, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yamada, T. Watanabe, N. Baba, Y. Takeuchi, F. Ohsawa, S. Gomi
Crystal Structures Of Biapenem And Tebipenem Complexed With Penicillin-Binding Proteins 2X And 1A From Streptococcus Pneumoniae
Antimicrob. Agents Chemother. V. 52 2053 2008
PubMed-ID: 18391040  |  Reference-DOI: 10.1128/AAC.01456-07
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2X
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 71-238
    Gene: PBPX
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Other Details: N-TERMINAL DOMAIN
    Synonym: PBP-2X, PBP2X
 
Molecule 2 - PENICILLIN-BINDING PROTEIN 2X
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 241-625
    Gene: PBPX
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Other Details: TRANSPEPTIDASE DOMAIN
    Synonym: PBP-2X, PBP2X
 
Molecule 3 - PENICILLIN-BINDING PROTEIN 2X
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 626-750
    Gene: PBPX
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Other Details: C-TERMINAL DOMAIN
    Synonym: PBP-2X, PBP2X

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TEB2Ligand/Ion(4R,5S)-3-(1-(4,5-DIHYDROTHIAZOL-2-YL)AZETIDIN-3-YLTHIO)-5-((2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL)-4-METHYL-4,5- DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2TEB1Ligand/Ion(4R,5S)-3-(1-(4,5-DIHYDROTHIAZOL-2-YL)AZETIDIN-3-YLTHIO)-5-((2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL)-4-METHYL-4,5- DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TEB1Ligand/Ion(4R,5S)-3-(1-(4,5-DIHYDROTHIAZOL-2-YL)AZETIDIN-3-YLTHIO)-5-((2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL)-4-METHYL-4,5- DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2TEB-1Ligand/Ion(4R,5S)-3-(1-(4,5-DIHYDROTHIAZOL-2-YL)AZETIDIN-3-YLTHIO)-5-((2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL)-4-METHYL-4,5- DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR E:425 , ARG E:426 , ARG F:654BINDING SITE FOR RESIDUE SO4 E 901
2AC2SOFTWARESER B:337 , TRP B:374 , SER B:395 , ASN B:397 , PHE B:450 , GLN B:452 , THR B:526 , LYS B:547 , SER B:548 , GLY B:549 , THR B:550 , LYS D:211BINDING SITE FOR RESIDUE TEB B 801
3AC3SOFTWAREGLU B:320 , SER E:337 , TRP E:374 , SER E:395 , ASN E:397 , PHE E:450 , GLN E:452 , THR E:526 , LYS E:547 , SER E:548 , GLY E:549 , THR E:550BINDING SITE FOR RESIDUE TEB E 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZC4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg B:307 -Pro B:308
2Ser B:576 -Pro B:577
3Arg E:307 -Pro E:308
4Ser E:576 -Pro E:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZC4)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRPN632-691
 
692-750
 		  4C:632-691
F:632-691
C:692-750
F:692-750
PBPX_STRR6632-691
 
692-750
 		  4C:632-691
F:632-691
C:692-750
F:692-750
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRPN632-691
 
692-750
 		  2C:632-691
-
C:692-750
-
PBPX_STRR6632-691
 
692-750
 		  2C:632-691
-
C:692-750
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRPN632-691
 
692-750
 		  2-
F:632-691
-
F:692-750
PBPX_STRR6632-691
 
692-750
 		  2-
F:632-691
-
F:692-750
Biological Unit 3 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRPN632-691
 
692-750
 		  4C:632-691
F:632-691
C:692-750
F:692-750
PBPX_STRR6632-691
 
692-750
 		  4C:632-691
F:632-691
C:692-750
F:692-750

(-) Exons   (0, 0)

(no "Exon" information available for 2ZC4)

(-) 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:158
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:158
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
           PBPX_STRPN    74 AKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTD 231
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeeeeeeee..................hhhhhhhhhhhhhh.hhhhhhhhhh.....eee.hhhhh..hhhhhhhhhhhhhh.....eeeeeeeeee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 A  74 AKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTD 231
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        


Chain A from PDB  Type:PROTEIN  Length:158
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:158
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
           PBPX_STRR6    74 AKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTD 231
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeeeeeeee..................hhhhhhhhhhhhhh.hhhhhhhhhh.....eee.hhhhh..hhhhhhhhhhhhhh.....eeeeeeeeee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 A  74 AKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTD 231
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        


Chain B from PDB  Type:PROTEIN  Length:366
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:366
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613      
           PBPX_STRPN   254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLN 619
               SCOP domains d2zc4b_ B: Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhhhhhhheeeeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhhh......eee...eee..eee.hhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.......hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zc4 B 254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLN 619
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613      


Chain B from PDB  Type:PROTEIN  Length:366
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:366
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613      
           PBPX_STRR6   254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLN 619
               SCOP domains d2zc4b_ B: Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhhhhhhheeeeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhhh......eee...eee..eee.hhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.......hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zc4 B 254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLN 619
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613      


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:125
                                   635       645       655       665       675       685       695       705       715       725       735       745     
           PBPX_STRPN   626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d2zc4c1 C:626-692                                                  d2zc4c2 C:693-750                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhh..eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeeee....eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PASTA  PDB: C:632-691 UniProt: 632-691                      PASTA  PDB: C:692-750 UniProt: 692-750                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 C 626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                   635       645       655       665       675       685       695       705       715       725       735       745     


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:125
                                   635       645       655       665       675       685       695       705       715       725       735       745     
           PBPX_STRR6   626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d2zc4c1 C:626-692                                                  d2zc4c2 C:693-750                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhh..eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeeee....eeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------PASTA  PDB: C:632-691 UniProt: 632-691                      PASTA  PDB: C:692-750 UniProt: 692-750                      PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 C 626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                   635       645       655       665       675       685       695       705       715       725       735       745     


Chain D from PDB  Type:PROTEIN  Length:126
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:160
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           PBPX_STRPN    73 PAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDG 232
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PBP_dimer-2zc4D01 D:73-232                                                                                                                                       Pfam domains (1)
           Pfam domains (2) PBP_dimer-2zc4D02 D:73-232                                                                                                                                       Pfam domains (2)
         Sec.struct. author ......ee.....eeeee..eeeeeee..-------------------------------hhhhhhhhhh.....eee.....eeehhhhhh.....---.....eeeeee..ee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 D  73 PAKRGTIYDRNGVPIAEDATSYNVYAVID-------------------------------EESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKE---AEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDG 232
                                    82        92        |-         -         -         -|      142       152       162      |  -|      182       192       202       212       222       232
                                                      101                             133                                 169 173                                                           


Chain D from PDB  Type:PROTEIN  Length:126
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:160
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           PBPX_STRR6    73 PAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDG 232
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PBP_dimer-2zc4D01 D:73-232                                                                                                                                       Pfam domains (1)
           Pfam domains (2) PBP_dimer-2zc4D02 D:73-232                                                                                                                                       Pfam domains (2)
         Sec.struct. author ......ee.....eeeee..eeeeeee..-------------------------------hhhhhhhhhh.....eee.....eeehhhhhh.....---.....eeeeee..ee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 D  73 PAKRGTIYDRNGVPIAEDATSYNVYAVID-------------------------------EESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKE---AEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDG 232
                                    82        92        |-         -         -         -|      142       152       162      |  -|      182       192       202       212       222       232
                                                      101                             133                                 169 173                                                           


Chain E from PDB  Type:PROTEIN  Length:365
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:367
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       
           PBPX_STRPN   254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRTMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL 620
               SCOP domains d2zc4e_ E: Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------Transpeptidase-2zc4E01 E:289-609                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Transpeptidase-2zc4E02 E:289-609                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (2)
         Sec.struct. author ..ee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhh.............eee..eee......--.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.......hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 E 254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVN--LTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL 620
                                   263       273       283       293       303       313       323       333       343       353       363       373   |  |383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       
                                                                                                                                                     377  |                                                                                                                                                                                                                                                
                                                                                                                                                        380                                                                                                                                                                                                                                                


Chain E from PDB  Type:PROTEIN  Length:365
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:367
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       
           PBPX_STRR6   254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL 620
               SCOP domains d2zc4e_ E: Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------Transpeptidase-2zc4E01 E:289-609                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Transpeptidase-2zc4E02 E:289-609                                                                                                                                                                                                                                                                                                 ----------- Pfam domains (2)
         Sec.struct. author ..ee..eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........................hhhhhhhhhhhhhhhh.............eee..eee......--.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh.......hhhhhhhhhhhhhh...ee....eeeeee....eeee....eee...hhhhhhhhhhhhhhhhhh.......................eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 E 254 RTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVN--LTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNL 620
                                   263       273       283       293       303       313       323       333       343       353       363       373   |  |383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       
                                                                                                                                                     377  |                                                                                                                                                                                                                                                
                                                                                                                                                        380                                                                                                                                                                                                                                                


Chain F from PDB  Type:PROTEIN  Length:125
 aligned with PBPX_STRPN | P14677 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:125
                                   635       645       655       665       675       685       695       705       715       725       735       745     
           PBPX_STRPN   626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d2zc4f1 F:626-692                                                  d2zc4f2 F:693-750                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------PASTA-2zc4F01 F:694-750                                   Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------PASTA-2zc4F02 F:694-750                                   Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeee.....ee...............eeee.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PASTA  PDB: F:632-691 UniProt: 632-691                      PASTA  PDB: F:692-750 UniProt: 692-750                      PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 F 626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                   635       645       655       665       675       685       695       705       715       725       735       745     


Chain F from PDB  Type:PROTEIN  Length:125
 aligned with PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:125
                                   635       645       655       665       675       685       695       705       715       725       735       745     
           PBPX_STRR6   626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d2zc4f1 F:626-692                                                  d2zc4f2 F:693-750                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------PASTA-2zc4F01 F:694-750                                   Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------PASTA-2zc4F02 F:694-750                                   Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhh...eeeee.....eeee............eeeeee............hhhhhhhhhhhhh.eeee.....ee...............eeee.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------PASTA  PDB: F:632-691 UniProt: 632-691                      PASTA  PDB: F:692-750 UniProt: 692-750                      PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc4 F 626 ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                   635       645       655       665       675       685       695       705       715       725       735       745
   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, 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 2ZC4)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)
(-)
Clan: no clan defined [family: PASTA] (12)
(-)
Clan: no clan defined [family: PBP_dimer] (15)

(-) Gene Ontology  (10, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (PBPX_STRPN | P14677)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B,C,D,E,F   (PBPX_STRR6 | P59676)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PBPX_STRPN | P14677: 1pmd 1qme 1qmf 1rp5 2z2l 2z2m 2zc3
        PBPX_STRR6 | P59676: 1pyy 2z2l 2z2m 2zc3

(-) Related Entries Specified in the PDB File

2zc3 2zc5 2zc6