2B5R - JenaLib

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Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   1B LACTAMASE / B LACTAMASE INHIBITOR

Authors :   O. Rahat, S. Albeck, R. Meged, O. Dym, G. Screiber, Israel Structural Proteomics Center (Ispc)

Date :   29 Sep 05 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Protein-Protein Complex, Structural Genomics, Israel Structural Proteomics Center, Ispc, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Reichmann, M. Cohen, R. Abramovich, O. Dym, D. Lim, N. C. Strynadka, G. Schreiber
Binding Hot Spots In The Tem1-Blip Interface In Light Of Its Modular Architecture.
J. Mol. Biol. V. 102 57 2006
PubMed-ID: 17070843 | Reference-DOI: 10.1016/J.JMB.2006.09.076
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE TEM
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BLA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TEM-1, TEM-2, TEM-3, TEM-4, TEM-5, TEM-6, TEM- 8/CAZ-2, TEM-16/CAZ-7, TEM-24/CAZ-6, IRT-4, PENICILLINASE

Molecule 2 - BETA-LACTAMASE INHIBITORY PROTEIN
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STREPTOMYCES CLAVULIGERUS
	Organism Taxid	:	1901
	Synonym	:	BLIP

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2B5R)

(no "Site" information available for 2B5R)

Asymmetric Unit

No.	Residues
1	A:77	-	A:123
2	B:77	-	B:123
3	C:1109	-	C:1131
4	D:1030	-	D:1042
5	D:1109	-	D:1131

Asymmetric Unit

No.	Residues
1	Glu A:166	-	Pro A:167
2	Tyr C:1119	-	Pro C:1120
3	Glu B:166	-	Pro B:167
4	Tyr D:1119	-	Pro D:1120

Asymmetric Unit (10, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_BLAT_ECOLX_002 *	Q	37	K	BLAT_ECOLX	---	---	A/B	Q	39	K
02	UniProt	VAR_BLAT_ECOLX_003 *	M	67	L	BLAT_ECOLX	---	---	A/B	M	69	L
03	UniProt	VAR_BLAT_ECOLX_004 *	E	102	K	BLAT_ECOLX	---	---	A/B	Y	104	K
04	UniProt	VAR_BLAT_ECOLX_005 *	R	162	H	BLAT_ECOLX	---	---	A/B	R	164	H
05	UniProt	VAR_BLAT_ECOLX_006 *	R	162	S	BLAT_ECOLX	---	---	A/B	R	164	S
06	UniProt	VAR_BLAT_ECOLX_007 *	A	235	T	BLAT_ECOLX	---	---	A/B	A	237	T
07	UniProt	VAR_BLAT_ECOLX_008 *	G	236	S	BLAT_ECOLX	---	---	A/B	G	238	S
08	UniProt	VAR_BLAT_ECOLX_009 *	E	237	K	BLAT_ECOLX	---	---	A/B	E	239	K
09	UniProt	VAR_BLAT_ECOLX_010 *	T	261	M	BLAT_ECOLX	---	---	A/B	T	263	M
10	UniProt	VAR_BLAT_ECOLX_011 *	N	272	D	BLAT_ECOLX	---	---	A/B	N	274	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (10, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_BLAT_ECOLX_002 *	Q	37	K	BLAT_ECOLX	---	---	A/B	Q	39	K
02	UniProt	VAR_BLAT_ECOLX_003 *	M	67	L	BLAT_ECOLX	---	---	A/B	M	69	L
03	UniProt	VAR_BLAT_ECOLX_004 *	E	102	K	BLAT_ECOLX	---	---	A/B	Y	104	K
04	UniProt	VAR_BLAT_ECOLX_005 *	R	162	H	BLAT_ECOLX	---	---	A/B	R	164	H
05	UniProt	VAR_BLAT_ECOLX_006 *	R	162	S	BLAT_ECOLX	---	---	A/B	R	164	S
06	UniProt	VAR_BLAT_ECOLX_007 *	A	235	T	BLAT_ECOLX	---	---	A/B	A	237	T
07	UniProt	VAR_BLAT_ECOLX_008 *	G	236	S	BLAT_ECOLX	---	---	A/B	G	238	S
08	UniProt	VAR_BLAT_ECOLX_009 *	E	237	K	BLAT_ECOLX	---	---	A/B	E	239	K
09	UniProt	VAR_BLAT_ECOLX_010 *	T	261	M	BLAT_ECOLX	---	---	A/B	T	263	M
10	UniProt	VAR_BLAT_ECOLX_011 *	N	272	D	BLAT_ECOLX	---	---	A/B	N	274	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (0, 0)

						dbSNP	PDB
No.	Source	Variant ID	Variant	UniProt ID	Status	ID	Chain	Variant

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	BLAT_ECOLX	64-79	2	A:66-81 B:66-81

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAT_ECOLX	64-79	2	A:66-81 B:66-81

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_A	PS00146	Beta-lactamase class-A active site.	BLAT_ECOLX	64-79	0	- -

(no "Exon" information available for 2B5R)

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:263
 aligned with BLAT_ECOLX | P62593 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:263
                                    33        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   
          BLAT_ECOLX     24 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  286
               SCOP domains d2b5ra1 A:26-288 beta-Lactamase, class A                                                                                                                                                                                                                                SCOP domains
               CATH domains 2b5rA00 A:26-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh...hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -------------K-----------------------------L----------------------------------K-----------------------------------------------------------H------------------------------------------------------------------------TSK-----------------------M----------D-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b5r A   26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVYNSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  288
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with BLAT_ECOLX | P62593 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:263
                                    33        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   
          BLAT_ECOLX     24 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  286
               SCOP domains d2b5rb_ B: beta-Lactamase, class A                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2b5rB00 B:26-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -------------K-----------------------------L----------------------------------K-----------------------------------------------------------H------------------------------------------------------------------------TSK-----------------------M----------D-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b5r B   26 HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVYNSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW  288
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with BLIP_STRCL | P35804 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:165
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     
          BLIP_STRCL     37 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV  201
               SCOP domains d2b5rc_ C: automated matches                                                                                                                                          SCOP domains
               CATH domains 2b5rC01 C:1001-1074  [code=3.30.1450.10, no name defined]                 2b5rC02 C:1075-1165  [code=3.30.1450.10, no name defined]                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....hhhhhhhhhh...ee.hhhhh..eeee.........eeeeee........eeeeeee..........hhhhhhhh....hhhhhhhhhh...eeeeeee..........eeeeeee.............eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b5r C 1001 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV 1165
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160

Chain D from PDB  Type:PROTEIN  Length:165
 aligned with BLIP_STRCL | P35804 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:165
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196     
          BLIP_STRCL     37 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV  201
               SCOP domains d2b5rd_ D: automated matches                                                                                                                                          SCOP domains
               CATH domains 2b5rD01 D:1001-1074  [code=3.30.1450.10, no name defined]                 2b5rD02 D:1075-1165  [code=3.30.1450.10, no name defined]                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....hhhhhhhhhh...ee.hhhhh..eeee.........eeeeee........eeeeeee..........hhhhhhhh....hhhhhhhhhh...eeeeeee..........eeeeeee.............eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2b5r D 1001 AGVMTGAKFTQIQFGMTRQQVLDIAGAENCETGGSFGDSIHCRGHAAGDYYAYATFGFTSAAADAKVDSKSQEKLLAPSAPTLTLAKFNQVTVGMTRAQVLATVGQGSCTTWSEYYPAYPSTAGVTLSLSCFDVDGYSSTGFYRGSAHLWFTDGVLQGKRQWDLV 1165
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta-lactamase Inhibitory Protein; Chain:B, domain 1 (13)

Homologous Superfamily: [code=3.30.1450.10, no name defined] (13)

Escherichia coli. Organism_taxid: 562. (4)

1a	2b5rC02	C:1075-1165
1b	2b5rD02	D:1075-1165
1c	2b5rC01	C:1001-1074
1d	2b5rD01	D:1001-1074

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

Topology: Beta-lactamase (339)

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

Escherichia coli. Organism_taxid: 562. (91)

2a	2b5rA00	A:26-288
2b	2b5rB00	B:26-288

(no "Pfam Domain" information available for 2B5R)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLAT_ECOLX | P62593)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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 C,D (BLIP_STRCL | P35804)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2b5r)

	Sites
(no "Sites" information available for 2b5r)

	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]
		Glu B:166 - Pro B:167	[ RasMol ]
		Tyr C:1119 - Pro C:1120	[ RasMol ]
		Tyr D:1119 - Pro D:1120	[ RasMol ]

Biological Units
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	2b5r
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(no "Related Entries Specified in the PDB File" available for 2B5R)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (4, 4)

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