2Y2O - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (EO9)

Authors :   C. Contreras-Martel, A. Amoroso, E. C. Woon, A. Zervosen, S. Inglis, A. O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. J. Schofield, A. D

Date :   15 Dec 10 (Deposition) - 03 Aug 11 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Transferase, Infection, Cell Wall, Peptidoglycan, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Contreras-Martel, A. Amoroso, E. C. Woon, A. Zervosen, S. Inglis, A. Martins, O. Verlaine, A. Rydzik, V. Job, A. Luxen, B. Joris, C. J. Schofield, A. Dessen
Structure-Guided Design Of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance In Staphylococcus Aureus (Mrsa).
Acs Chem. Biol. V. 6 943 2011
PubMed-ID: 21732689 | Reference-DOI: 10.1021/CB2001846

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
	Chains	:	A
	EC Number	:	2.4.1.129, 2.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYS
	Expression System Vector	:	PGEX
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	171101
	Other Details	:	ALKYL BORONATE (E09) COVALENTLY BOND TO S460
	Strain	:	R6
	Synonym	:	PBP1B

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 17)

No.	Name	Count	Type	Full Name
1	CL	14	Ligand/Ion	CHLORIDE ION
2	EO9	1	Ligand/Ion	(S)-(1-(2,6-DIFLUOROBENZAMIDO)ETHYL)BORONICACID
3	NA	1	Ligand/Ion	SODIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EO9	2	Ligand/Ion	(S)-(1-(2,6-DIFLUOROBENZAMIDO)ETHYL)BORONICACID
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:459 , SER A:460 , TYR A:498 , SER A:516 , ASN A:518 , GLY A:653 , THR A:654 , THR A:655 , GLY A:656 , ASP A:658 , NA A:1300 , HOH A:2080	BINDING SITE FOR RESIDUE EO9 A1000
02	AC2	SOFTWARE	THR A:563 , LYS A:583 , HOH A:2199 , HOH A:2200 , HOH A:2201 , HOH A:2202 , HOH A:2203 , HOH A:2204	BINDING SITE FOR RESIDUE SO4 A1100
03	AC3	SOFTWARE	ARG A:529 , HOH A:2101	BINDING SITE FOR RESIDUE CL A1200
04	AC4	SOFTWARE	VAL A:535 , LYS A:536	BINDING SITE FOR RESIDUE CL A1201
05	AC5	SOFTWARE	ARG A:627 , LYS A:633	BINDING SITE FOR RESIDUE CL A1202
06	AC6	SOFTWARE	ALA A:592 , ASP A:593 , ARG A:595	BINDING SITE FOR RESIDUE CL A1206
07	AC7	SOFTWARE	TYR A:544 , GLU A:545 , HOH A:2199	BINDING SITE FOR RESIDUE CL A1211
08	AC8	SOFTWARE	GLU A:346 , HIS A:584 , VAL A:585 , ILE A:586	BINDING SITE FOR RESIDUE CL A1212
09	AC9	SOFTWARE	ASP A:337 , TYR A:338 , LEU A:339 , HIS A:399 , GLN A:403	BINDING SITE FOR RESIDUE CL A1213
10	BC1	SOFTWARE	LYS A:610	BINDING SITE FOR RESIDUE CL A1214
11	BC2	SOFTWARE	TYR A:110 , ASP A:112 , GLN A:396 , HOH A:2026	BINDING SITE FOR RESIDUE CL A1216
12	BC3	SOFTWARE	LYS A:760 , SER A:761	BINDING SITE FOR RESIDUE CL A1217
13	BC4	SOFTWARE	ASP A:679 , ASP A:680 , HOH A:2147	BINDING SITE FOR RESIDUE CL A1222
14	BC5	SOFTWARE	THR A:342 , ASN A:449 , HOH A:2008	BINDING SITE FOR RESIDUE CL A1224
15	BC6	SOFTWARE	ARG A:358 , ASN A:645	BINDING SITE FOR RESIDUE CL A1227
16	BC7	SOFTWARE	THR A:652 , GLY A:653 , THR A:654 , EO9 A:1000	BINDING SITE FOR RESIDUE NA A1300
17	BC8	SOFTWARE	SER A:634	BINDING SITE FOR RESIDUE CL A1791

(no "SS Bond" information available for 2Y2O)

(no "Cis Peptide Bond" information available for 2Y2O)

(no "SAP(SNP)/Variant" information available for 2Y2O)

(no "PROSITE Motif" information available for 2Y2O)

(no "Exon" information available for 2Y2O)

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:471
 aligned with Q7CRA4_STRR6 | Q7CRA4 from UniProtKB/TrEMBL  Length:821

    Alignment length:686
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
         Q7CRA4_STRR6   105 ISEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eeee.-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee...................hhhhhhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeee.....eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhhh...............eeeeee........eee....eee....eeeeee.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2o A 105 ISEITYSDGTVIASI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSL 790
                                   114    |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -|      344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784      
                                        119                                                                                                                                                                                                                     335

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 '\|'

(no "SCOP Domain" information available for 2Y2O)

(no "CATH Domain" information available for 2Y2O)

(no "Pfam Domain" information available for 2Y2O)

Asymmetric Unit(hide GO term definitions)

Chain A (Q7CRA4_STRR6 | Q7CRA4)

molecular function
	GO:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
	GO:0008955	peptidoglycan glycosyltransferase activity	Catalysis of the reaction: [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-diphosphoundecaprenol + GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = [GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EO9	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y2o)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	2y2o
		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
	Q7CRA4_STRR6 \| Q7CRA4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	2.3.2.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	2.4.1.129
		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
	Q7CRA4_STRR6 \| Q7CRA4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2uwx	ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd1	ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASS A PENICILLIN-BINDING PROTEINS
2xd5	STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF STREPTOCOCCUS PNEUMONIAE PBP1B
2y2g	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (A01)
2y2h	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA2)
2y2i	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA3)
2y2j	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA4)
2y2k	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)
2y2l	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E06)
2y2m	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E08)
2y2n	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E07)
2y2p	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z10)
2y2q	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (Z06)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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