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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CARBENICILLIN
 
Authors :  S. Sainsbury, L. Bird, D. I. Stuart, R. J. Owens, J. Ren, Oxford Protein Production Facility (Oppf)
Date :  10 Aug 10  (Deposition) - 10 Nov 10  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Penicillin-Binding Proteins, Pseudomonas Aeruginosa, Carbenicillin, Structural Genomics, Oxford Protein Production Facility, Oppf, Transpeptidase, Cell Wall Biosynthesis, Out Periplasmic Membrane, Penicillin-Binding Protein-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sainsbury, L. Bird, V. Rao, S. M. Shepherd, D. I. Stuart, W. N. Hunter R. J. Owens, J. Ren
Crystal Structures Of Penicillin-Binding Protein 3 From Pseudomonas Aeruginosa: Comparison Of Native And Antibiotic-Bound Forms
J. Mol. Biol. V. 405 173 2011
PubMed-ID: 20974151  |  Reference-DOI: 10.1016/J.JMB.2010.10.024

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OPPF6502
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 35-579
    Gene: PA4418
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PAO1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CB91Ligand/Ion(2R,4S)-2-[(1R)-1-{[(2S)-2-CARBOXY-2-PHENYLACETYL]AMINO}-2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:387 , VAL A:388 , GLY A:389BINDING SITE FOR RESIDUE CL A 578
2AC2SOFTWARESER A:294 , VAL A:333 , SER A:349 , ASN A:351 , TYR A:409 , SER A:485 , GLY A:486 , THR A:487 , TYR A:501 , HOH A:593 , HOH A:650BINDING SITE FOR RESIDUE CB9 A 1
3AC3SOFTWAREGLY A:247 , SER A:248 , ARG A:284 , PHE A:290 , VAL A:521 , ASP A:523 , HOH A:585BINDING SITE FOR RESIDUE GOL A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OCL)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:200 -Gly A:201
2Gln A:265 -Pro A:266
3Tyr A:319 -Pro A:320
4Ala A:509 -Pro A:510

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OCL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OCL)

(-) Exons   (0, 0)

(no "Exon" information available for 3OCL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:498
 aligned with Q51504_PSEAI | Q51504 from UniProtKB/TrEMBL  Length:579

    Alignment length:509
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552         
         Q51504_PSEAI    53 VRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLP 561
               SCOP domains d3ocla1 A:53-221 automated matches                                                                                                                                       d3ocla2 A:222-559 automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....eeeeeeehhhhhhhhhhh....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhhh..eeeeeee.....ee-eeeeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeee.----------..eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ocl A  53 VRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVI-DVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARK----------NAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLP 559
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 | |   212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       | -       500       510       520       530       540       550         
                                                                                                                                                                                 204 |                                                                                                                                                                                                                                                                                         490        499                                                            
                                                                                                                                                                                   206
   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, 2)

Asymmetric/Biological 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 3OCL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OCL)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q51504_PSEAI | Q51504)
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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q51504_PSEAI | Q51504: 3pbr 3pbt
UniProtKB/TrEMBL
        Q51504_PSEAI | Q51504: 3oc2 3ocn 3pbn 3pbo 3pbq 3pbs 4fsf 4l0l 5df7 5df8 5df9

(-) Related Entries Specified in the PDB File

3oc2 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA
3ocn CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CEFTAZIDIME