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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH AZLOCILLIN
 
Authors :  J. Ren, J. E. Nettleship, A. Males, D. I. Stuart, R. J. Owens
Date :  26 Aug 15  (Deposition) - 13 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Azlocillin, Beta-Lactam Antibiotics, Acyl-Enzyme Complex, De- Acylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ren, J. E. Nettleship, A. Males, D. I. Stuart, R. J. Owens
Crystal Structures Of Penicillin-Binding Protein 3 In Complexes With Azlocillin And Cefoperazone In Both Acylated And Deacylated Forms.
Febs Lett. V. 590 288 2016
PubMed-ID: 26823174  |  Reference-DOI: 10.1002/1873-3468.12054

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN
    Chains: A, B
    EC Number: 2.4.1.129
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: PBPB, FTSI_2, ERS445055_04698, PAE221_03076, YQ19_27590
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PENICILLIN-BINDING PROTEIN 3,PSEUDOMONAS AERUGINOSA GENOME ASSEMBLY PAE221

 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, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
159H2Ligand/Ion(2R,4S)-5,5-DIMETHYL-2-[(1R)-2-OXO-1-{[(2R)-2-{[(2-OXOIMIDAZOLIDIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}ETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2CL4Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4IMD2Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
159H1Ligand/Ion(2R,4S)-5,5-DIMETHYL-2-[(1R)-2-OXO-1-{[(2R)-2-{[(2-OXOIMIDAZOLIDIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}ETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
159H1Ligand/Ion(2R,4S)-5,5-DIMETHYL-2-[(1R)-2-OXO-1-{[(2R)-2-{[(2-OXOIMIDAZOLIDIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}ETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:294 , TYR A:328 , 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 , PHE A:533 , GLY A:534 , HOH A:716 , HOH A:726 , HOH A:841binding site for residue 59H A 601
02AC2SOFTWAREGLY A:247 , SER A:248 , ARG A:284 , PHE A:290 , ARG A:504 , VAL A:523 , ASP A:525 , HOH A:731 , HOH A:757binding site for residue GOL A 602
03AC3SOFTWAREARG A:499 , ASN A:501binding site for residue CL A 603
04AC4SOFTWAREALA A:181 , PHE A:182 , LEU A:381binding site for residue IMD A 604
05AC5SOFTWAREGLY B:247 , SER B:248 , ARG B:284 , PHE B:290 , ALA B:415 , VAL B:523 , ASP B:525 , HOH B:701binding site for residue GOL B 602
06AC6SOFTWARETYR B:268 , ASN B:269 , ASN B:272 , ARG B:273 , HOH B:716binding site for residue GOL B 603
07AC7SOFTWAREARG A:175 , ARG B:473binding site for residue CL B 604
08AC8SOFTWARELYS B:490 , VAL B:491 , ARG B:504binding site for residue CL B 605
09AC9SOFTWAREARG A:473 , ARG B:175 , HOH B:802binding site for residue CL B 606
10AD1SOFTWAREALA B:181 , PHE B:182 , LEU B:381 , HOH B:792binding site for residue IMD B 607
11AD2SOFTWAREPRO B:292 , GLY B:293 , THR B:295 , VAL B:296 , LYS B:297 , TYR B:328 , VAL B:333 , SER B:349 , ASN B:351 , TYR B:407 , TYR B:409 , LYS B:484 , SER B:485 , GLY B:486 , THR B:487 , ALA B:488 , ARG B:489 , TYR B:498 , PHE B:533 , GLY B:534 , HOH B:712 , HOH B:714 , HOH B:818binding site for Di-peptide 59H B 601 and SER B 294

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DF7)

(-) 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 5DF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DF7)

(-) Exons   (0, 0)

(no "Exon" information available for 5DF7)

(-) 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:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhhh....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee.....eeeeeeeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5df7 A  50 ARSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTAT 564
                                    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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.hhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5df7 B  57 AIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTA 563
                                    66        76        86        96       106       116       126       136       146       156       166       176       186      |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
                                                                                                                                                                  193|                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                   211
   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  (0, 0)

(no "SCOP Domain" information available for 5DF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DF7)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q51504_PSEAI | Q51504: 3pbr 3pbt
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        Q51504_PSEAI | Q51504: 3oc2 3ocl 3ocn 3pbn 3pbo 3pbq 3pbs 4fsf 4l0l 5df8 5df9

(-) Related Entries Specified in the PDB File

4kqo PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH PIPERACILLIN