3HBR - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXA-48 BETA-LACTAMASE

Authors :   V. Calderone, S. Mangani, M. Benvenuti, G. M. Rossolini, J. D. Docquier

Date :   05 May 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: C  (1x)
Biol. Unit 6: D  (1x)

Keywords :   Class D Beta-Lactamase, Oxa-48, Antibiotic, Dimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Docquier, V. Calderone, F. De Luca, M. Benvenuti, F. Giuliani, L. Bellucci, A. Tafi, P. Nordmann, M. Botta, G. M. Rossolini, S. Mangani
Crystal Structure Of The Oxa-48 Beta-Lactamase Reveals Mechanistic Diversity Among Class D Carbapenemases.
Chem. Biol. V. 16 540 2009
PubMed-ID: 19477418 | Reference-DOI: 10.1016/J.CHEMBIOL.2009.04.010
(for further references see the PDB file header)

Molecule 1 - OXA-48
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9A
	Expression System Strain	:	DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BLA OXA-48
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573
	Strain	:	11978

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B
Biological Unit 5 (1x)	:			C
Biological Unit 6 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 5 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:198 , ALA A:199 , ASN A:200 , ALA B:199	BINDING SITE FOR RESIDUE EDO A 266
2	AC2	SOFTWARE	THR B:197 , GLU B:198 , TRP B:222 , GLN B:251 , LYS B:255 , HOH B:456	BINDING SITE FOR RESIDUE EDO B 266
3	AC3	SOFTWARE	TRP B:25 , TRP B:47 , HOH B:399	BINDING SITE FOR RESIDUE EDO B 267
4	AC4	SOFTWARE	PHE C:142 , ASP C:143 , SER C:171 , PHE C:172 , LYS C:175 , HOH C:286	BINDING SITE FOR RESIDUE EDO C 266

(no "SS Bond" information available for 3HBR)

Asymmetric Unit

No.	Residues
1	Glu A:216	-	Pro A:217
2	Glu B:216	-	Pro B:217
3	Glu C:216	-	Pro C:217
4	Glu D:216	-	Pro D:217

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

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

(no "Exon" information available for 3HBR)

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:240
 aligned with Q6XEC0_KLEPN | Q6XEC0 from UniProtKB/TrEMBL  Length:265

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
         Q6XEC0_KLEPN    25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
               SCOP domains d3hbra_ A: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hbrA00 A:25-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh......-....hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hbr A  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDI-GNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144    | |154       164       174       184       194       204       214       224       234       244       254       264 
                                                                           73-KCX                                                                     149 |                                                                                                                  
                                                                                                                                                        151

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with Q6XEC0_KLEPN | Q6XEC0 from UniProtKB/TrEMBL  Length:265

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
         Q6XEC0_KLEPN    25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
               SCOP domains d3hbrb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hbrB00 B:25-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhh...eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hbr B  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
                                                                           73-KCX

Chain C from PDB  Type:PROTEIN  Length:240
 aligned with Q6XEC0_KLEPN | Q6XEC0 from UniProtKB/TrEMBL  Length:265

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
         Q6XEC0_KLEPN    25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
               SCOP domains d3hbrc_ C: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 3hbrC00 C:25-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeeeeee....eeee...hhhhh...hhhhhhhhhhhhhhhhh..............-..hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hbr C  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQ-RDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94   | | 104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
                                                                           73-KCX                   98 |                                                                                                                                                                     
                                                                                                     100

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with Q6XEC0_KLEPN | Q6XEC0 from UniProtKB/TrEMBL  Length:265

    Alignment length:241
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
         Q6XEC0_KLEPN    25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
               SCOP domains d3hbrd_ D: automated matc  hes                                                                                                                                                                                                                    SCOP domains
               CATH domains 3hbrD00 D:25-265 DD-pepti  dase/beta-lactamase superfamily                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhh..eeeeeee.--.eeee...hhhh.ee.hhhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hbr D  25 WQENKSWNAHFTEHKSQGVVVLWNE--QQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44    |  |54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
                                                   49 52                   73-KCX

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)

Klebsiella pneumoniae [TaxId: 573] (4)

1a	d3hbra_	A:
1b	d3hbrb_	B:
1c	d3hbrc_	C:
1d	d3hbrd_	D:

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)

Klebsiella pneumoniae. Organism_taxid: 573. Strain: 11978. (1)

1a	3hbrB00	B:25-265
1b	3hbrA00	A:25-265
1c	3hbrC00	C:25-265
1d	3hbrD00	D:25-265

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q6XEC0_KLEPN | Q6XEC0)

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.
	GO:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
	GO:0017001	antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	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:216 - Pro A:217	[ RasMol ]
		Glu B:216 - Pro B:217	[ RasMol ]
		Glu C:216 - Pro C:217	[ RasMol ]
		Glu D:216 - Pro D:217	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3HBR)

Description

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Ligands, Modified Residues, Ions (2, 8)

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SS Bonds (0, 0)

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