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Biological Unit 4 (Jmol Viewer)

Title :   BLAC AMOXICILLIN ACYL-INTERMEDIATE COMPLEX

Authors :   J. A. Mire, Tb Structural Genomics Consortium (Tbsgc)

Date :   23 Mar 12 (Deposition) - 03 Apr 13 (Release) - 03 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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 :   Ambler Class A Beta-Lactamase, Beta-Lactamase, Serine Hydrolase, Esterase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Mire, P. Pai, N. Siddiqi, D. H. Russell, E. J. Rubin, J. C. Sacchettini
Faropenem Is Effective Against Mycobacterium Tuberculosis I Vitro And In Vivo
To Be Published
PubMed: search

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BLAA, BLAC, MT2128, MTCY49.07C, RV2068C
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	PENICILLINASE

		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 (2, 8)

No.	Name	Count	Type	Full Name
1	AXL	2	Ligand/Ion	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	AXL	-1	Ligand/Ion	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AXL	1	Ligand/Ion	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	AXL	1	Ligand/Ion	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	AXL	-1	Ligand/Ion	2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:70 , SER A:130 , THR A:216 , THR A:235 , THR A:237 , GLN B:110 , GLN B:111	BINDING SITE FOR RESIDUE PO4 A 301
2	AC2	SOFTWARE	ASP A:124 , ARG A:213	BINDING SITE FOR RESIDUE PO4 A 302
3	AC3	SOFTWARE	LEU A:88 , ASP A:202 , LYS A:203	BINDING SITE FOR RESIDUE PO4 A 303
4	AC4	SOFTWARE	CYS B:69 , SER B:70 , SER B:130 , ASN B:170 , THR B:235 , GLY B:236 , THR B:237	BINDING SITE FOR RESIDUE AXL B 301
5	AC5	SOFTWARE	SER C:70 , SER C:130 , ASN C:170 , THR C:235 , THR C:237	BINDING SITE FOR RESIDUE AXL C 301
6	AC6	SOFTWARE	ASP C:124 , ARG C:128 , ARG C:213	BINDING SITE FOR RESIDUE PO4 C 302
7	AC7	SOFTWARE	GLN C:111 , SER D:130 , THR D:216 , THR D:235 , GLY D:236 , THR D:237	BINDING SITE FOR RESIDUE PO4 D 301
8	AC8	SOFTWARE	ASP D:124 , ARG D:128 , ARG D:213	BINDING SITE FOR RESIDUE PO4 D 302

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

Asymmetric Unit

No.	Residues
1	Ala A:166	-	Pro A:167
2	Ala C:166	-	Pro C:167
3	Ala D:166	-	Pro D:167

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

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

(no "Exon" information available for 4EBN)

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:265
                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeee........eee.....ee....hhhhhhhhhhh....hhhh.ee.....................eehhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee.....eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ebn A   29 DLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVAAVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSDGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDAEAPELNRDPPGDERDTTTPHAIALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATCVAGVLA  293
                                    38        48        58        68        78    ||  90       100       110       120       130       140     ||146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288     
                                                                                 83|                                                        145A|||                                                                                          238|         252|                                       
                                                                                  86                                                         145B||                                                                                           240          254                                       
                                                                                                                                              145C|                                                                                                                                                  
                                                                                                                                               145D

Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeee........eee.....ee....hhhhhhhhhhhh.hhhhhh.ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee.....eeeeeeeeehhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ebn B   29 DLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVAAVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSDGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDAEAPELNRDPPGDERDTTTPHAIALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATCVAGVLA  293
                                    38        48        58        68        78    ||  90       100       110       120       130       140     ||146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288     
                                                                                 83|                                                        145A|||                                                                                          238|         252|                                       
                                                                                  86                                                         145B||                                                                                           240          254                                       
                                                                                                                                              145C|                                                                                                                                                  
                                                                                                                                               145D

Chain C from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeee........eee.....ee.hhhhhhhhhhhhhhhhhhhhhh.ee..hhhhh......hhhhh...eehhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh...........hhhhhh.......eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee.....eeeeeeeee..........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ebn C   29 DLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVAAVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSDGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDAEAPELNRDPPGDERDTTTPHAIALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATCVAGVLA  293
                                    38        48        58        68        78    ||  90       100       110       120       130       140     ||146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288     
                                                                                 83|                                                        145A|||                                                                                          238|         252|                                       
                                                                                  86                                                         145B||                                                                                           240          254                                       
                                                                                                                                              145C|                                                                                                                                                  
                                                                                                                                               145D

Chain D from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeeee........eee.....ee.hhhhhhhhhhhhhhh.hhhhhh.ee............hhhhhh...eehhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh............hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee.....eeeeeeeee..........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ebn D   29 DLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVAAVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSDGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDAEAPELNRDPPGDERDTTTPHAIALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATCVAGVLA  293
                                    38        48        58        68        78    ||  90       100       110       120       130       140     ||146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288     
                                                                                 83|                                                        145A|||                                                                                          238|         252|                                       
                                                                                  86                                                         145B||                                                                                           240          254                                       
                                                                                                                                              145C|                                                                                                                                                  
                                                                                                                                               145D

Legend:		→ Mismatch	(orange background)
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	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 '\|'

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

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

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

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Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:166 - Pro A:167	[ RasMol ]
		Ala C:166 - Pro C:167	[ RasMol ]
		Ala D:166 - Pro D:167	[ RasMol ]

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	4ebn
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3vff	BLAC E166A CDC-OME ACYL-INTERMEDIATE COMPLEX
3vfh	BLAC E166A CDC-1 ACYL-INTERMEDIATE COMPLEX
4ebi	BLAC TEBIPENEM ACYL-INTERMEDIATE COMPLEX
4ebl	BLAC E166A FAROPENEM ACYL-INTERMEDIATE COMPLEX
4ebm	BLAC BIAPENEM ACYL-INTERMEDIATE COMPLEX
4ebo	BLAC E166A CEFOPERAZONE ACYL-INTERMEDIATE COMPLEX
4ebp	BLAC E166A CEFOTAXIME ACYL-INTERMEDIATE COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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