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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH PIPERACILLIN
 
Authors :  J. E. Nettleship, D. I. Stuart, R. J. Owens, J. Ren
Date :  15 May 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Penicillin-Binding Proteins, Piperacillin, Cell Wall Biosynthesis, Transpeptidase, Out Periplasmic Membrane, Biosynthetic Protein- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Van Berkel, J. E. Nettleship, I. K. Leung, J. Brem, H. Choi, D. I. Stuart, T. D. Claridge, M. A. Mcdonough, R. J. Owens, J. Ren, C. J. Schofield
Binding Of (5S)-Penicilloic Acid To Penicillin Binding Protein 3.
Acs Chem. Biol. V. 8 2112 2013
PubMed-ID: 23899657  |  Reference-DOI: 10.1021/CB400200H

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FTSI, PA4418
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 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  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4JPP2Ligand/IonPIPERACILLIN (OPEN FORM)
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3IMD-1Ligand/IonIMIDAZOLE
4JPP1Ligand/IonPIPERACILLIN (OPEN FORM)
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4JPP1Ligand/IonPIPERACILLIN (OPEN FORM)

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:294 , TYR A:328 , VAL A:333 , SER A:349 , ASN A:351 , TYR A:409 , SER A:485 , GLY A:486 , THR A:487 , ALA A:488 , ARG A:489 , TYR A:498 , GLY A:534 , HOH A:732 , HOH A:829 , HOH A:847 , HOH A:849BINDING SITE FOR RESIDUE JPP A 601
2AC2SOFTWAREGLY A:247 , SER A:248 , ARG A:284 , PHE A:290 , ASP A:525 , HOH A:704BINDING SITE FOR RESIDUE GOL A 602
3AC3SOFTWARESER A:435 , MET A:436 , THR A:437BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWARESER B:294 , TYR B:328 , VAL B:333 , SER B:349 , ASN B:351 , TYR B:409 , LYS B:484 , SER B:485 , GLY B:486 , THR B:487 , ARG B:489 , TYR B:498 , HOH B:706 , HOH B:762 , HOH B:819BINDING SITE FOR RESIDUE JPP B 601
5AC5SOFTWAREGLY B:247 , SER B:248 , ARG B:284 , PHE B:290 , VAL B:523 , ASP B:525BINDING SITE FOR RESIDUE GOL B 602
6AC6SOFTWAREARG B:551 , ASN B:554BINDING SITE FOR RESIDUE IMD B 603
7AC7SOFTWARELYS B:490 , VAL B:491 , ARG B:504BINDING SITE FOR RESIDUE CL B 604
8AC8SOFTWAREARG B:152 , ARG B:273 , ARG B:274BINDING SITE FOR RESIDUE CL B 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln A:265 -Pro A:266
2Tyr A:319 -Pro A:320
3Ala A:511 -Pro A:512
4Gln B:265 -Pro B:266
5Tyr B:319 -Pro B:320
6Ala B:511 -Pro B:512

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KQO)

(-) 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:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kqoa1 A:50-221 automated matches                                                                                                                                          d4kqoa2 A:222-562 automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee.....eeeeeeeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqo A  50 ARSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPT 562
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559   


Chain B from PDB  Type:PROTEIN  Length:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4kqob1 B:58-221 automated matches                                                                                                                  d4kqob2 B:222-563 automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhh...............ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqo B  58 IPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTA 563
                                    67        77        87        97       107       117       127       137       147       157       167       177       187    || 213       223       233       243       253       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
                                                                                                                                                                192|                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                 209
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (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 4KQO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        FTSI_PSEAE | G3XD46: 3pbn 3pbo 3pbq 3pbr 3pbs 3pbt 4kqq 4kqr

(-) Related Entries Specified in the PDB File

4kqq 4kqr