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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CEFOPERAZONE
 
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 :  Cefoperazone, 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  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
159F2Ligand/Ion(2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-(4-HYDROXYPHENYL)ACETYL]AMINO}-2-OXOETHYL]-5-METHYL-1,3-THIAZINANE-4-CARBOXYLIC ACID
2CL6Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
159F1Ligand/Ion(2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-(4-HYDROXYPHENYL)ACETYL]AMINO}-2-OXOETHYL]-5-METHYL-1,3-THIAZINANE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
159F1Ligand/Ion(2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-(4-HYDROXYPHENYL)ACETYL]AMINO}-2-OXOETHYL]-5-METHYL-1,3-THIAZINANE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:294 , TYR A:328 , VAL A:333 , SER A:349 , ASN A:351 , TYR A:407 , TYR A:409 , LYS A:484 , SER A:485 , GLY A:486 , THR A:487 , ALA A:488 , ARG A:489 , TYR A:498 , TYR A:532 , HOH A:737 , HOH A:773 , HOH A:814 , HOH A:873binding site for residue 59F A 601
02AC2SOFTWAREGLY A:247 , SER A:248 , ARG A:284 , PHE A:290 , ASP A:525 , HOH A:766 , HOH A:837binding site for residue GOL A 602
03AC3SOFTWAREGLU A:176 , PRO A:278 , ARG A:282 , HOH A:832 , HOH A:870 , ARG B:473 , GOL B:603binding site for residue GOL A 603
04AC4SOFTWARETYR A:268 , ASN A:269 , ASN A:272 , ARG A:273 , ASN A:275 , LEU A:276binding site for residue GOL A 604
05AC5SOFTWAREARG A:387 , VAL A:388binding site for residue CL A 605
06AC6SOFTWARESER A:435 , MET A:436 , THR A:437binding site for residue CL A 606
07AC7SOFTWAREVAL A:491 , ARG A:504binding site for residue CL A 607
08AC8SOFTWAREGLY B:247 , SER B:248 , ARG B:284 , PHE B:290 , ARG B:504 , VAL B:523 , ASP B:525 , HOH B:754binding site for residue GOL B 602
09AC9SOFTWAREARG A:282 , GOL A:603 , HOH A:870 , GLU B:234 , ALA B:238 , GLU B:241binding site for residue GOL B 603
10AD1SOFTWAREARG A:473 , LEU A:536 , HOH A:716 , GLU B:176 , PRO B:278 , MET B:281 , ARG B:282 , HOH B:706binding site for residue GOL B 604
11AD2SOFTWAREHIS B:232 , ARG B:236 , GLN B:265 , THR B:267binding site for residue CL B 605
12AD3SOFTWAREVAL B:491 , ARG B:504binding site for residue CL B 606
13AD4SOFTWAREASN B:501binding site for residue CL B 607
14AD5SOFTWAREPRO 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:409 , LYS B:484 , SER B:485 , GLY B:486 , THR B:487 , ALA B:488 , ARG B:489 , TYR B:498 , TYR B:503 , TYR B:532 , PHE B:533 , GLY B:534 , HOH B:729 , HOH B:760 , HOH B:807 , HOH B:826 , HOH B:868binding site for Di-peptide 59F B 601 and SER B 294

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DF8)

(-) 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 5DF8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DF8)

(-) Exons   (0, 0)

(no "Exon" information available for 5DF8)

(-) 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:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5df8 A  51 RSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTAT 564
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560    


Chain B from PDB  Type:PROTEIN  Length:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5df8 B  57 AIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPT 562
                                    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         
                                                                                                                                                                  193|                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                   211
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DF8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DF8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DF8)

(-) Gene Ontology  (4, 4)

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  2.4.1.129
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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 5df7 5df9

(-) Related Entries Specified in the PDB File

5df7 CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH AZLOCILLIN