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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NATIVE, DI-ZINC METALLO-BETA-LACTAMASE IMP-1
 
Authors :  J. Spencer, P. Hinchliffe
Date :  19 Nov 15  (Deposition) - 01 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Inhibitor, Carbapenemase, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Hinchliffe, M. M. Gonzalez, M. F. Mojica, J. M. Gonzalez, V. Castillo, C. Saiz, M. Kosmopoulou, C. L. Tooke, L. I. Llarrull, G. Mahler, R. A. Bonomo, A. J. Vila, J. Spencer
Cross-Class Metallo-Beta-Lactamase Inhibition By Bisthiazolidines Reveals Multiple Binding Modes.
Proc. Natl. Acad. Sci. Usa V. 113 E3745 2016
PubMed-ID: 27303030  |  Reference-DOI: 10.1073/PNAS.1601368113

(-) Compounds

Molecule 1 - BETA-LACTAMASE IMP-1
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: POPIN-F
    Expression System Taxid: 469008
    Expression System Variant: SOLU
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Synonym: BLAIMP,BETA-LACTAMASE TYPE II,PENICILLINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:77 , HIS A:79 , HIS A:139 , ZN A:302 , HOH A:478binding site for residue ZN A 301
02AC2SOFTWAREASP A:81 , CYS A:158 , HIS A:197 , ZN A:301 , HOH A:426 , HOH A:478binding site for residue ZN A 302
03AC3SOFTWAREGLU A:14 , GLY A:15 , LEU A:39 , GLU A:150 , ARG A:151 , HOH A:438binding site for residue EDO A 303
04AC4SOFTWARESER A:99 , PHE A:118 , SER A:119 , GLY A:120 , TYR A:134 , VAL A:144 , HOH A:413 , HOH A:495 , HOH A:498binding site for residue ACT A 304
05AC5SOFTWAREHIS B:77 , HIS B:79 , HIS B:139 , ZN B:302 , HOH B:476binding site for residue ZN B 301
06AC6SOFTWAREASP B:81 , CYS B:158 , HIS B:197 , ZN B:301 , HOH B:476binding site for residue ZN B 302
07AC7SOFTWAREGLU B:14 , VAL B:38 , LEU B:39 , GLU B:150 , ARG B:151 , HOH B:444binding site for residue EDO B 303
08AC8SOFTWAREASP C:81 , CYS C:158 , HIS C:197 , ZN C:302 , HOH C:515binding site for residue ZN C 301
09AC9SOFTWAREHIS C:77 , HIS C:79 , HIS C:139 , ZN C:301 , HOH C:515binding site for residue ZN C 302
10AD1SOFTWAREHIS D:77 , HIS D:79 , HIS D:139 , ZN D:302 , HOH D:429binding site for residue ZN D 301
11AD2SOFTWAREASP D:81 , CYS D:158 , HIS D:197 , ZN D:301 , HOH D:429binding site for residue ZN D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EV6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn D:26 -Gly D:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EV6)

(-) Exons   (0, 0)

(no "Exon" information available for 5EV6)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eeee..eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ev6 A   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ev6 B  -1 GPAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   


Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ev6 C   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSK 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ev6 D   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   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 5EV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EV6)

(-) Gene Ontology  (7, 7)

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 Related Entries

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        BLAB_SERMA | P52699: 1dd6 1jje 1jjt 1vgn 1wuo 1wup 2doo 4c1f 4c1g 5ev8 5ewa 5hh4

(-) Related Entries Specified in the PDB File

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