3BFG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH MEROPENEM

Authors :   L. Pernot, S. Petrella, W. Sougakoff

Date :   21 Nov 07 (Deposition) - 18 Dec 07 (Release) - 16 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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, Beta-Lactamase, Class A, Sed-G238C, Meropenem, Acyl-Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Pernot, S. Petrella, W. Sougakoff
Acyl-Intermediate Structures Of The Class A Beta-Lactamase Sed-G238C
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CLASS A BETA-LACTAMASE SED1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET29A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	SED-G238C, UNP RESIDUES 34-295
	Gene	:	BLA-SED-1
	Mutation	:	YES
	Organism Scientific	:	CITROBACTER SEDLAKII
	Organism Taxid	:	67826
	Strain	:	2596

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MER	4	Ligand/Ion	(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MER	1	Ligand/Ion	(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MER	1	Ligand/Ion	(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	MER	1	Ligand/Ion	(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	MER	1	Ligand/Ion	(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:69 , SER A:70 , SER A:130 , ASN A:132 , GLU A:166 , ASN A:170 , THR A:216 , LYS A:234 , THR A:235 , GLY A:236 , ALA A:237 , TRP A:274 , LYS A:276 , HOH A:354 , HOH A:412 , HOH A:427	BINDING SITE FOR RESIDUE MER A 301
2	AC2	SOFTWARE	CYS B:69 , SER B:70 , LYS B:73 , TRP B:105 , SER B:130 , ASN B:132 , THR B:216 , LYS B:234 , THR B:235 , GLY B:236 , ALA B:237 , HOH B:376 , HOH B:439	BINDING SITE FOR RESIDUE MER B 302
3	AC3	SOFTWARE	CYS C:69 , SER C:70 , LYS C:73 , TRP C:105 , SER C:130 , ASN C:132 , GLU C:166 , THR C:216 , LYS C:234 , THR C:235 , GLY C:236 , ALA C:237 , HOH C:471 , HOH C:499 , THR D:86	BINDING SITE FOR RESIDUE MER C 303
4	AC4	SOFTWARE	CYS D:69 , SER D:70 , LYS D:73 , TRP D:105 , SER D:130 , ASN D:132 , THR D:216 , LYS D:234 , THR D:235 , GLY D:236 , ALA D:237 , HOH D:352 , HOH D:425	BINDING SITE FOR RESIDUE MER D 304

Asymmetric Unit

No.	Residues
1	A:69	-	A:238
2	B:69	-	B:238
3	C:69	-	C:238
4	D:69	-	D:238

Asymmetric Unit

No.	Residues
1	Glu A:166	-	Pro A:167
2	Glu B:166	-	Pro B:167
3	Glu C:166	-	Pro C:167
4	Glu D:166	-	Pro D:167

(no "SAP(SNP)/Variant" information available for 3BFG)

(no "PROSITE Motif" information available for 3BFG)

(no "Exon" information available for 3BFG)

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:262
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:262
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
         Q93PQ0_9ENTR    34 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfga_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3bfgA00 A:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhhhh.hhhh.eee...........hhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfg A  26 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:262
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
         Q93PQ0_9ENTR    34 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfgb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3bfgB00 B:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh....hhhh.eeeehhhhh.....hhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfg B  26 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254

Chain C from PDB  Type:PROTEIN  Length:262
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:262
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
         Q93PQ0_9ENTR    34 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfgc_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3bfgC00 C:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhh....hhhh.eeee..........hhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfg C  26 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 240          254

Chain D from PDB  Type:PROTEIN  Length:262
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:262
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
         Q93PQ0_9ENTR    34 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfgd_ D: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3bfgD00 D:26-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eee.hhhhh.....hhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfg D  26 VQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    35        45        55 ||     66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                          57|                                                                                                                                                                                238|         252|                                    
                                                           59                                                                                                                                                                                 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: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: automated matches (81)

Citrobacter sedlakii [TaxId: 67826] (5)

1a	d3bfga_	A:
1b	d3bfgc_	C:
1c	d3bfgd_	D:
1d	d3bfgb_	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)

Citrobacter sedlakii. Organism_taxid: 67826. Strain: 2596. (5)

1a	3bfgA00	A:26-290
1b	3bfgC00	C:26-290
1c	3bfgD00	D:26-290
1d	3bfgB00	B:26-290

(no "Pfam Domain" information available for 3BFG)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q93PQ0_9ENTR | Q93PQ0)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]
		Glu B:166 - Pro B:167	[ RasMol ]
		Glu C:166 - Pro C:167	[ RasMol ]
		Glu D:166 - Pro D:167	[ RasMol ]

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	3bfg
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	Q93PQ0_9ENTR \| Q93PQ0
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	3.5.2.6
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	Q93PQ0_9ENTR \| Q93PQ0
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UniProtKB/TrEMBL
	Q93PQ0_9ENTR \| Q93PQ0	:	3bfc 3bfd 3bfe 3bff

3bfc	CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH IMIPENEM
3bfd	CLASS A BETA-LACTAMASE SED-G238C
3bfe	CLASS A BETA-LACTAMASE SED-1
3bff	CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH FAROPENEM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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