2Q9M - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   4-SUBSTITUTED TRINEMS AS BROAD SPECTRUM-LACTAMASE INHIBITORS: STRUCTURE-BASED DESIGN, SYNTHESIS AND BIOLOGICAL ACTIVITY

Authors :   I. Plantan, L. Selic, T. Mesar, P. Stefanic Anderluh, M. Oblak, A. Prezelj, L. Hesse, M. Andrejasic, M. Vilar, D. Turk, A. Kocijan, T. Prevec, G. Vilfan, D. Kocjan, A. Copar, U. Urleb, T. Solmajer

Date :   13 Jun 07 (Deposition) - 21 Aug 07 (Release) - 31 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym./Biol. Unit : A

Keywords :   Beta-Lactamase Inhibitor, Tricyclic Carbapenem, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Plantan, L. Selic, T. Mesar, P. S. Anderluh, M. Oblak, A. Prezelj, L. Hesse, M. Andrejasic, M. Vilar, D. Turk, A. Kocijan, T. Prevec, G. Vilfan, D. Kocjan, A. Copar, U. Urleb, T. Solmajer
4-Substituted Trinems As Broad Spectrum Beta-Lactamase Inhibitors: Structure-Based Design, Synthesis, And Biological Activity
J. Med. Chem. V. 50 4113 2007
PubMed-ID: 17665896 | Reference-DOI: 10.1021/JM0703237
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE
	Chains	:	A
	EC Number	:	3.5.2.6
	Organism Scientific	:	ENTEROBACTER CLOACAE
	Organism Taxid	:	550
	Strain	:	908R
	Synonym	:	CEPHALOSPORINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	LK7	1	Ligand/Ion	(1R,4S,7AS)-1-(1-FORMYLPROP-1-EN-1-YL)-4-METHOXY-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:64 , TYR A:150 , ASN A:152 , SER A:289 , LEU A:293 , GLY A:317 , SER A:318 , HOH A:548 , HOH A:706 , HOH A:714	BINDING SITE FOR RESIDUE LK7 A 0

(no "SS Bond" information available for 2Q9M)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:276	-	Pro A:277
2	Asn A:302	-	Pro A:303

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AMPC_ENTCL_004 *	I	36	V	AMPC_ENTCL	---	---	A	I	16	V
2	UniProt	VAR_AMPC_ENTCL_005 *	P	58	S	AMPC_ENTCL	---	---	A	P	38	S
3	UniProt	VAR_AMPC_ENTCL_006 *	A	108	P	AMPC_ENTCL	---	---	A	A	88	P
4	UniProt	VAR_AMPC_ENTCL_007 *	L	152	V	AMPC_ENTCL	---	---	A	L	132	V
5	UniProt	VAR_AMPC_ENTCL_008 *	N	262	K	AMPC_ENTCL	---	---	A	N	242	K
6	UniProt	VAR_AMPC_ENTCL_009 *	A	319	V	AMPC_ENTCL	---	---	A	A	299	V
7	UniProt	VAR_AMPC_ENTCL_010 *	T	362	K	AMPC_ENTCL	---	---	A	T	342	K
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_C	PS00336	Beta-lactamase class-C active site.	AMPC_ENTCL	80-87	1	A:60-67

(no "Exon" information available for 2Q9M)

Asymmetric/Biological 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:359
 aligned with AMPC_ENTCL | P05364 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:359
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
           AMPC_ENTCL    22 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 380
               SCOP domains d2q9ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2q9mA00 A:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------Beta-lactamase-2q9mA01 A:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhhh..............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhh..ee....ee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhh.hhhhhh..ee.eeeeeee.....eeeeeeee....eeeeee.hhh.eeeeeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9m A   2 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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/Biological 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)

Enterobacter cloacae [TaxId: 550] (3)

d2q9ma_

Asymmetric/Biological 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)

Enterobacter cloacae. Organism_taxid: 550. Strain: 908r (1)

2q9mA00

A:2-360

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Beta-lactamase (79)

Enterobacter cloacae (8)

Beta-lactamase-2q9mA01

A:12-360

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AMPC_ENTCL | P05364)

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: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.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		LK7	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:302 - Pro A:303	[ RasMol ]
		Trp A:276 - Pro A:277	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2q9m
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AMPC_ENTCL \| P05364
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.2.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	AMPC_ENTCL \| P05364
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	AMPC_ENTCL \| P05364	:	1bls 1gce 1rgz 1xx2 1y54 2q9n 3s4x 4xux 5hai

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File