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(-) Description

Title :  CRYSTAL STRUCTURE OF KPC-2 BETA-LACTAMASE IN COMPLEX WITH THE S02030 BORONIC ACID INHIBITOR
 
Authors :  N. Q. Nguyen, F. Van Den Akker
Date :  22 Oct 15  (Deposition) - 03 Feb 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transition State Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Q. Nguyen, N. P. Krishnan, L. J. Rojas, F. Prati, E. Caselli, C. Romagnoli, R. A. Bonomo, F. Van Den Akker
Crystal Structures Of Kpc-2 And Shv-1 Beta-Lactamases In Complex With The Boronic Acid Transition State Analog S02030.
Antimicrob. Agents Chemother. V. 60 1760 2016
PubMed-ID: 26729491  |  Reference-DOI: 10.1128/AAC.02643-15

(-) Compounds

Molecule 1 - CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLA, KPC, KPC1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC-1

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2ZXM2Ligand/Ion1-{(2R)-2-(DIHYDROXYBORANYL)-2-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOLE-4-CARBOXYLIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZXM1Ligand/Ion1-{(2R)-2-(DIHYDROXYBORANYL)-2-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOLE-4-CARBOXYLIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZXM1Ligand/Ion1-{(2R)-2-(DIHYDROXYBORANYL)-2-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-1H-1,2,3-TRIAZOLE-4-CARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:69 , SER A:70 , TRP A:105 , SER A:130 , ASN A:132 , GLU A:166 , LEU A:167 , LEU A:169 , ASN A:170 , THR A:235 , THR A:237 , CYS A:238 , GLY A:239 , SO4 A:304 , HOH A:401 , HOH A:411 , LYS B:140binding site for residue ZXM A 301
2AC2SOFTWARESER A:59 , ARG A:61 , ALA A:62 , GLU A:63 , HOH A:408 , HOH A:516binding site for residue SO4 A 302
3AC3SOFTWARESER A:275 , GLU A:276 , ALA A:277 , HOH A:508 , HOH A:515binding site for residue SO4 A 303
4AC4SOFTWAREARG A:220 , HIS A:274 , GLU A:276 , ZXM A:301 , HOH A:411binding site for residue SO4 A 304
5AC5SOFTWARESER B:275 , GLU B:276 , ALA B:277 , HOH B:403 , HOH B:432 , HOH B:486binding site for residue SO4 B 303
6AC6SOFTWARESER B:43 , ARG B:61 , HOH B:405 , HOH B:423 , HOH B:479 , HOH B:509 , HOH B:516binding site for residue SO4 B 304

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:69 -A:238
2B:69 -B:238

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:166 -Leu A:167
2Glu B:166 -Leu B:167
3Leu B:290 -Gly B:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EEC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EEC)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh........ee..hhhhh...hhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eec A  25 LTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG 291
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |256       266       276       286     
                                                           57|                                                                                                                                                                                              252|                                     
                                                            59                                                                                                                                                                                               254                                     


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh........ee..hhhhh.....hhhhhh...eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eec B  25 LTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLG 291
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |256       266       276       286     
                                                           57|                                                                                                                                                                                              252|                                     
                                                            59                                                                                                                                                                                               254
   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 5EEC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  5eec
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  BLKPC_KLEPN | Q9F663
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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLKPC_KLEPN | Q9F663: 2ov5 3e2k 3e2l 3rxw 3rxx 4zbe 5uj3 5uj4 5ul8

(-) Related Entries Specified in the PDB File

5ee8