4PVO - JenaLib

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Title :   CRYSTAL STRUCTURE OF VIM-2 METALLO-BETA-LACTAMASE IN COMPLEX WITH ML302 AND ML302F

Authors :   W. S. Aik, J. Brem, M. A. Mcdonough, C. J. Schofield

Date :   18 Mar 14 (Deposition) - 19 Nov 14 (Release) - 25 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

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

Keywords :   Alpha-Beta/Beta-Alpha Fold, Beta-Lactamase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Brem, S. S. Van Berkel, W. Aik, A. M. Rydzik, M. B. Avison, I. Pettinati, K. D. Umland, A. Kawamura, J. Spencer, T. D. Claridge, M. A. Mcdonough, C. J. Schofield
Rhodanine Hydrolysis Leads To Potent Thioenolate Mediated Metallo-Beta-Lactamase Inhibition.
Nat. Chem. V. 6 1084 2014
PubMed-ID: 25411887 | Reference-DOI: 10.1038/NCHEM.2110

Molecule 1 - BETA-LACTAMASE CLASS B VIM-2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POPIN-F VIM-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 27-266
	Gene	:	BLA-VIM-2, BLASVIM-2, BLAVIM-2, BLAVIM2, VIM-2
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	CLASS B BETA-LACTAMASE, METALLO BETA-LACTAMASE, METALLO- BETA-LACTAMASE, METALLO-BETA-LACTAMASE VIM-2, METTALO-BETA-LACTAMASE VIM-2, VIM-2, VIM-2 CLASS B METALLO B-LACTAMASE, 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 (5, 14)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	4	Ligand/Ion	FORMIC ACID
3	S3C	2	Ligand/Ion	(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4	SVB	1	Ligand/Ion	N-(4-METHYLPIPERAZIN-1-YL)-2-[(5Z)-4-OXO-2-THIOXO-5-(2,3,6-TRICHLOROBENZYLIDENE)-1,3-THIAZOLIDIN-3-YL]ACETAMIDE
5	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	2	Ligand/Ion	FORMIC ACID
3	S3C	1	Ligand/Ion	(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4	SVB	1	Ligand/Ion	N-(4-METHYLPIPERAZIN-1-YL)-2-[(5Z)-4-OXO-2-THIOXO-5-(2,3,6-TRICHLOROBENZYLIDENE)-1,3-THIAZOLIDIN-3-YL]ACETAMIDE
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
2	FMT	2	Ligand/Ion	FORMIC ACID
3	S3C	1	Ligand/Ion	(2Z)-2-SULFANYL-3-(2,3,6-TRICHLOROPHENYL)PROP-2-ENOICACID
4	SVB	-1	Ligand/Ion	N-(4-METHYLPIPERAZIN-1-YL)-2-[(5Z)-4-OXO-2-THIOXO-5-(2,3,6-TRICHLOROBENZYLIDENE)-1,3-THIAZOLIDIN-3-YL]ACETAMIDE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:116 , HIS A:118 , HIS A:196 , S3C A:403	BINDING SITE FOR RESIDUE ZN A 401
02	AC2	SOFTWARE	ASP A:120 , CYS A:221 , HIS A:263 , S3C A:403	BINDING SITE FOR RESIDUE ZN A 402
03	AC3	SOFTWARE	TRP A:87 , HIS A:118 , ASP A:120 , HIS A:196 , CYS A:221 , ARG A:228 , ASN A:233 , HIS A:263 , ZN A:401 , ZN A:402 , SVB A:404 , HOH A:501 , HOH A:507	BINDING SITE FOR RESIDUE S3C A 403
04	AC4	SOFTWARE	PHE A:61 , TYR A:67 , GLY A:232 , ASN A:233 , HIS A:263 , S3C A:403 , GLY B:63	BINDING SITE FOR RESIDUE SVB A 404
05	AC5	SOFTWARE	HIS A:170 , HIS A:285 , FMT A:406 , FMT A:407	BINDING SITE FOR RESIDUE ZN A 405
06	AC6	SOFTWARE	THR A:169 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:405 , FMT A:407 , HOH A:568 , HOH A:757	BINDING SITE FOR RESIDUE FMT A 406
07	AC7	SOFTWARE	ALA A:135 , HIS A:170 , HIS A:285 , ASN A:288 , ZN A:405 , FMT A:406 , HOH A:739	BINDING SITE FOR RESIDUE FMT A 407
08	AC8	SOFTWARE	PRO A:107 , VAL A:109 , HOH A:546 , HOH A:746	BINDING SITE FOR RESIDUE DMS A 408
09	AC9	SOFTWARE	HIS B:116 , HIS B:118 , HIS B:196 , ZN B:402 , S3C B:406	BINDING SITE FOR RESIDUE ZN B 401
10	BC1	SOFTWARE	ASP B:120 , CYS B:221 , HIS B:263 , ZN B:401 , S3C B:406	BINDING SITE FOR RESIDUE ZN B 402
11	BC2	SOFTWARE	HIS B:170 , FMT B:404 , FMT B:405	BINDING SITE FOR RESIDUE ZN B 403
12	BC3	SOFTWARE	ALA B:135 , HIS B:170 , ZN B:403 , FMT B:405 , HOH B:545	BINDING SITE FOR RESIDUE FMT B 404
13	BC4	SOFTWARE	ALA B:135 , THR B:169 , HIS B:170 , ZN B:403 , FMT B:404 , HOH B:510	BINDING SITE FOR RESIDUE FMT B 405
14	BC5	SOFTWARE	TRP B:87 , HIS B:116 , HIS B:118 , ASP B:120 , HIS B:196 , CYS B:221 , ARG B:228 , ASN B:233 , HIS B:263 , ZN B:401 , ZN B:402 , HOH B:506	BINDING SITE FOR RESIDUE S3C B 406

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

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

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

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

(no "Exon" information available for 4PVO)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               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
                 4pvo A  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR 296
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285       295 
                                          45|               64|                               100|  107|                   131|              150|                                     205| ||                                               265|                   
                                           47                66                                102   109                    133               165                                      209 ||                                                277                   
                                                                                                                                                                                         211|                                                                      
                                                                                                                                                                                          215

Chain B from PDB  Type:PROTEIN  Length:233
                                                                                                                                                                                                                                                                         
               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
                 4pvo B  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSV 298
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285       295   
                                          45|               64|                               100|  107|                   131|              150|                                     205| ||                                               265|                     
                                           47                66                                102   109                    133               165                                      209 ||                                                277                     
                                                                                                                                                                                         211|                                                                        
                                                                                                                                                                                          215

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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

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

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

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