1W7F - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE BS3 INHIBITED WITH ISOCITRATE

Authors :   S. Petrella, E. Sauvage, R. Herman, P. Charlier

Date :   01 Sep 04 (Deposition) - 24 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Hydrolase, Beta-Lactamase, Isocitrate, Bacillus Licheniformis Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Petrella, E. Sauvage, R. Herman, P. Charlier
Crystal Structure Of The Class A Beta-Lactamase Bs3 Bs3 Inhibited With Isocitrate
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Organism Scientific	:	BACILLUS LICHENIFORMIS
	Organism Taxid	:	1402
	Strain	:	BS3

		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 (1, 1)

No.	Name	Count	Type	Full Name
1	ICT	1	Ligand/Ion	ISOCITRIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ICT	1	Ligand/Ion	ISOCITRIC ACID

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ICT	-1	Ligand/Ion	ISOCITRIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:69 , SER A:70 , LYS A:73 , TYR A:105 , SER A:130 , THR A:216 , THR A:235 , GLY A:236 , ALA A:237 , ARG A:244 , HOH A:2035 , HOH A:2107 , HOH A:2119	BINDING SITE FOR RESIDUE ICT A1291

(no "SS Bond" information available for 1W7F)

Asymmetric Unit

No.	Residues
1	Glu A:166	-	Pro A:167
2	Glu B:166	-	Pro B:167

(no "SAP(SNP)/Variant" information available for 1W7F)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	2	A:66-81 B:66-81

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	1	A:66-81 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAC_BACLI	82-97	1	- B:66-81

(no "Exon" information available for 1W7F)

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:256
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:256
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297      
           BLAC_BACLI    48 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d1w7fa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w7fA00 A:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7f A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254

Chain A from PDB  Type:PROTEIN  Length:256
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:256
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d1w7fa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w7fA00 A:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7f A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:256
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297      
           BLAC_BACLI    48 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains d1w7fb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w7fB00 B:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
           Pfam domains (1) --Beta-lactamase-1w7fB01 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --Beta-lactamase-1w7fB02 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh..hhhh.ee............hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7f B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:256
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d1w7fb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w7fB00 B:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
           Pfam domains (1) --Beta-lactamase-1w7fB01 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --Beta-lactamase-1w7fB02 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh..hhhh.ee............hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7f B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: automated matches (70)

Protein domain: automated matches (70)

Bacillus licheniformis [TaxId: 1402] (1)

1a	d1w7fa_	A:
1b	d1w7fb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Beta-lactamase (339)

Homologous Superfamily: DD-peptidase/beta-lactamase superfamily (335)

Bacillus licheniformis. Organism_taxid: 1402. Strain: bs3 (4)

1a	1w7fA00	A:31-291
1b	1w7fB00	B:31-291

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Beta-lactamase (79)

Bacillus licheniformis (7)

1a	Beta-lactamase-1w7fB01	B:33-284
1b	Beta-lactamase-1w7fB02	B:33-284

Asymmetric Unit(hide GO term definitions)

Chain A,B (P94458_BACLI | P94458)

molecular function
	GO:0008800	beta-lactamase activity	Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
	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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Chain A,B (BLAC_BACLI | P00808)

molecular function
	GO:0008800	beta-lactamase activity	Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
	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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	BLAC_BACLI \| P00808	:	1i2s 1i2w 1mbl 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz
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	P94458_BACLI \| P94458	:	2x71 4a5r

(no "Related Entries Specified in the PDB File" available for 1W7F)

Description

Compounds

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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