4C1D - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH L-CAPTOPRIL

Authors :   D. Zollman, J. Brem, M. A. Mcdonough, S. S. Vanberkel, C. J. Schofield

Date :   12 Aug 13 (Deposition) - 27 Aug 14 (Release) - 13 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Brem, S. S. Van Berkel, D. Zollman, S. Y. Lee, O. Gileadi, P. J. Mchugh, T. R. Walsh, M. A. Mcdonough, C. J. Schofield
Structural Basis Of Metallo-Beta-Lactamase Inhibition By Captopril Stereoisomers.
Antimicrob. Agents Chemother. V. 60 142 2015
PubMed-ID: 26482303 | Reference-DOI: 10.1128/AAC.01335-15

Molecule 1 - BETA-LACTAMASE CLASS B VIM-2
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	OPINF VECTOR BASED ON PTRIEX VECTOR
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Fragment	:	RESIDUES 2-240
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	PLASMID DERIVED NON-GENOMIC.
	Synonym	:	CLASS B BETA-LACTAMASE, METALLO BETA LACTAMASE VIM-2, METALLO BETA-LACTAMASE, METALLO-BETA-LACTAMASE, METALLO-BETA-LACTAMASE VIM-2, METTALO-BETA-LACTAMASE VIM-2, VIM-2, VIM-2 PROTEIN, VIM-2 TYPE METALLO-BETA-LACTAMASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	NA	2	Ligand/Ion	SODIUM ION
3	X8Z	2	Ligand/Ion	L-CAPTOPRIL
4	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION
3	X8Z	1	Ligand/Ion	L-CAPTOPRIL
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION
3	X8Z	1	Ligand/Ion	L-CAPTOPRIL
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:171 , HIS A:229 , HOH A:2139 , HOH A:2140	BINDING SITE FOR RESIDUE NA A 300
02	AC2	SOFTWARE	PHE A:62 , TRP A:87 , HIS A:116 , ASP A:118 , HIS A:179 , ASN A:210 , ZN A:501 , ZN A:502 , HOH A:2168 , HOH A:2225	BINDING SITE FOR RESIDUE X8Z A 350
03	AC3	SOFTWARE	ALA A:132 , THR A:133 , THR A:152 , HIS A:153 , HIS A:251 , ASN A:254 , FMT A:401 , ZN A:503 , HOH A:2095 , HOH A:2206	BINDING SITE FOR RESIDUE FMT A 400
04	AC4	SOFTWARE	ALA A:132 , HIS A:153 , HIS A:251 , ASN A:254 , FMT A:400 , ZN A:503	BINDING SITE FOR RESIDUE FMT A 401
05	AC5	SOFTWARE	HIS A:114 , HIS A:116 , HIS A:179 , X8Z A:350	BINDING SITE FOR RESIDUE ZN A 501
06	AC6	SOFTWARE	ASP A:118 , ARG A:119 , CYS A:198 , HIS A:240 , X8Z A:350	BINDING SITE FOR RESIDUE ZN A 502
07	AC7	SOFTWARE	HIS A:153 , HIS A:251 , FMT A:400 , FMT A:401	BINDING SITE FOR RESIDUE ZN A 503
08	AC8	SOFTWARE	GLU B:171 , HIS B:229 , HOH B:2128 , HOH B:2129 , HOH B:2205	BINDING SITE FOR RESIDUE NA B 300
09	AC9	SOFTWARE	TYR B:67 , TRP B:87 , HIS B:116 , ASP B:118 , HIS B:179 , ASN B:210 , ZN B:501 , ZN B:502 , HOH B:2156	BINDING SITE FOR RESIDUE X8Z B 350
10	BC1	SOFTWARE	ALA B:132 , HIS B:153 , FMT B:401 , ZN B:503 , HOH B:2083 , HOH B:2206	BINDING SITE FOR RESIDUE FMT B 400
11	BC2	SOFTWARE	ALA B:132 , THR B:133 , THR B:152 , HIS B:153 , FMT B:400 , ZN B:503 , HOH B:2081	BINDING SITE FOR RESIDUE FMT B 401
12	BC3	SOFTWARE	HIS B:114 , HIS B:116 , HIS B:179 , X8Z B:350	BINDING SITE FOR RESIDUE ZN B 501
13	BC4	SOFTWARE	ASP B:118 , CYS B:198 , HIS B:240 , X8Z B:350	BINDING SITE FOR RESIDUE ZN B 502
14	BC5	SOFTWARE	HIS B:153 , FMT B:400 , FMT B:401	BINDING SITE FOR RESIDUE ZN B 503

(no "SS Bond" information available for 4C1D)

(no "Cis Peptide Bond" information available for 4C1D)

(no "SAP(SNP)/Variant" information available for 4C1D)

(no "PROSITE Motif" information available for 4C1D)

(no "Exon" information available for 4C1D)

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:232
 aligned with Q9K2N0_PSEAI | Q9K2N0 from UniProtKB/TrEMBL  Length:266

    Alignment length:232
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
         Q9K2N0_PSEAI    32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 263
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1d A  32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q9K2N0_PSEAI | Q9K2N0 from UniProtKB/TrEMBL  Length:266

    Alignment length:232
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  
         Q9K2N0_PSEAI    32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 263
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c1d B  32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS 263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 '\|'

(no "SCOP Domain" information available for 4C1D)

(no "CATH Domain" information available for 4C1D)

(no "Pfam Domain" information available for 4C1D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9K2N0_PSEAI | Q9K2N0)

molecular function
	GO:0016787		hydrolase activity		Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		X8Z	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c1d)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4c1d
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	3.5.2.6
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		Disease Information	:	OMIM

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UniProtKB/Swiss-Prot
	Q9K2N0_PSEAI \| Q9K2N0	:	5k48 5n4s 5n4t 5nhz 5ni0
UniProtKB/TrEMBL
	Q9K2N0_PSEAI \| Q9K2N0	:	1ko2 1ko3 4bz3 4c1e 4nq2 4pvo 4pvt 4ua4 5acu 5acv 5acw 5acx 5fqc 5lca 5lcf 5lch 5le1 5lm6

4bz3	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2
4c09	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE BCII WITH L-CAPTOPRIL
4c1c	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE BCII WITH D-CAPTOPRIL
4c1e	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH D-CAPTOPRIL
4c1f	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE IMP-1 WITH L-CAPTOPRIL
4c1g	CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE IMP-1 WITH D-CAPTOPRIL
4c1h	CRYSTAL STRUCTURE OF A BETA LACTAMASE IN COMPLEX WITH AN INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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Related Entries

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