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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE NDM-1 IN COMPLEX WITH A BISTHIAZOLIDINE INHIBITOR
 
Authors :  M. Kosmopoulou, P. Hinchliffe, J. Spencer
Date :  23 Jul 14  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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 :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kosmopoulou, P. Hinchliffe, J. Spencer
Crystal Structure Of The Metallo-Beta-Lactamase Ndm-1 In Complex With A Bisthiazolidine Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE NDM-1
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: POPINF
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: BLANDM-1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: NDM-1,METALLO-BETA-LACTAMASE NDM-1

 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
13C74Ligand/Ion(3R,5R,7AS)-5-(SULFANYLMETHYL)TETRAHYDRO[1,3]THIAZOLO[4,3-B][1,3]THIAZOLE-3-CARBOXYLIC ACID
2GOL2Ligand/IonGLYCEROL
3ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13C71Ligand/Ion(3R,5R,7AS)-5-(SULFANYLMETHYL)TETRAHYDRO[1,3]THIAZOLO[4,3-B][1,3]THIAZOLE-3-CARBOXYLIC ACID
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13C71Ligand/Ion(3R,5R,7AS)-5-(SULFANYLMETHYL)TETRAHYDRO[1,3]THIAZOLO[4,3-B][1,3]THIAZOLE-3-CARBOXYLIC ACID
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
13C71Ligand/Ion(3R,5R,7AS)-5-(SULFANYLMETHYL)TETRAHYDRO[1,3]THIAZOLO[4,3-B][1,3]THIAZOLE-3-CARBOXYLIC ACID
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
13C71Ligand/Ion(3R,5R,7AS)-5-(SULFANYLMETHYL)TETRAHYDRO[1,3]THIAZOLO[4,3-B][1,3]THIAZOLE-3-CARBOXYLIC ACID
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , 3C7 A:303binding site for residue ZN A 301
02AC2SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , 3C7 A:303binding site for residue ZN A 302
03AC3SOFTWAREHIS A:122 , ASP A:124 , HIS A:189 , HIS A:250 , ZN A:301 , ZN A:302 , HOH A:480 , HOH A:562 , HOH A:563binding site for residue 3C7 A 303
04AC4SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , 3C7 B:303binding site for residue ZN B 301
05AC5SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , 3C7 B:303binding site for residue ZN B 302
06AC6SOFTWAREHIS B:122 , ASP B:124 , HIS B:189 , HIS B:250 , ZN B:301 , ZN B:302 , HOH B:485 , HOH B:525 , HOH B:561binding site for residue 3C7 B 303
07AC7SOFTWAREASP C:124 , CYS C:208 , HIS C:250 , 3C7 C:304binding site for residue ZN C 301
08AC8SOFTWAREHIS C:120 , HIS C:122 , HIS C:189 , 3C7 C:304binding site for residue ZN C 302
09AC9SOFTWAREPRO A:150 , GLY A:153 , ARG C:234 , GLY C:237 , ALA C:238 , ARG C:256 , HOH C:412binding site for residue GOL C 303
10AD1SOFTWAREVAL C:73 , TRP C:93 , HIS C:122 , ASP C:124 , HIS C:189 , HIS C:250 , ZN C:301 , ZN C:302 , HOH C:482 , HOH C:499 , HOH C:550 , HOH C:553binding site for residue 3C7 C 304
11AD2SOFTWAREASP D:124 , CYS D:208 , HIS D:250 , 3C7 D:304binding site for residue ZN D 301
12AD3SOFTWAREHIS D:120 , HIS D:122 , HIS D:189 , 3C7 D:304binding site for residue ZN D 302
13AD4SOFTWAREPRO B:150 , GLY B:153 , ARG D:234 , GLY D:237 , ALA D:238 , ARG D:256 , ILE D:259 , THR D:260 , HOH D:537binding site for residue GOL D 303
14AD5SOFTWAREHIS D:122 , HIS D:189 , ASN D:220 , HIS D:250 , ZN D:301 , ZN D:302 , HOH D:642binding site for residue 3C7 D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U4L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U4L)

(-) Exons   (0, 0)

(no "Exon" information available for 4U4L)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeee..eeeeeeee....eeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhh.........eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4l A  39 METGDQRFGDLVFRQLAPNVWQHTSYLDMGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    48        58        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
                                                       67|                                                                                                                                                                                                       
                                                        71                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4l B  40 ETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeeee..eeeeeee....eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4l C  43 DQRFGDLVFRQLAPNVWQHTSYLDMVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    52        62    ||  77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   
                                                   67|                                                                                                                                                                                                     
                                                    73                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeee..eeeeeee...eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4l D  41 TGDQRFGDLVFRQLAPNVWQHTSYLDVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    50        60     || 76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266    
                                                    66|                                                                                                                                                                                                     
                                                     73
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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 4U4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U4L)

(-) Gene Ontology  (7, 7)

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        BLAN1_KLEPN | C7C422: 3pg4 3q6x 3rkj 3rkk 3sbl 3sfp 3spu 3srx 3zr9 4exs 4exy 4ey2 4eyb 4eyf 4eyl 4gyq 4gyu 4h0d 4hky 4hl1 4hl2 4ram 4raw 4rbs 4rl0 4rl2 4rm5 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

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