4EMW - JenaLib

Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS BOUND WITH THE COVALENT INHIBITOR ETVC-COA

Authors :   J. S. Edwards, B. D. Wallace, A. Claiborne, M. R. Redinbo

Date :   12 Apr 12 (Deposition) - 17 Oct 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Wallace, J. S. Edwards, J. R. Wallen, W. J. Moolman, R. Van Der Westhuyzen, E. Strauss, M. R. Redinbo, A. Claiborne
Turnover-Dependent Covalent Inactivation Of Staphylococcus Aureus Coenzyme A-Disulfide Reductase By Coenzyme A-Mimetics: Mechanistic And Structural Insights.
Biochemistry V. 51 7699 2012
PubMed-ID: 22954034 | Reference-DOI: 10.1021/BI301026C

Compounds

Molecule 1 - COENZYME A DISULFIDE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.8.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	T7, PXCDR
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CDR, SAUSA300_0873
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	367830
	Strain	:	USA300
	Synonym	:	COA-DISULFIDE REDUCTASE, COADR

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CAJ	2	Ligand/Ion	ETHYL 5-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-3,3-DIMETHYL-2-OXIDANYL-BUTANOYL]AMINO]PROPANOYLAMINO]PENTANOATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	MG	2	Ligand/Ion	MAGNESIUM ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:7 , GLY A:8 , VAL A:10 , ALA A:11 , GLY A:12 , PHE A:32 , GLU A:33 , LYS A:34 , ASP A:35 , ASN A:42 , CYS A:43 , HIS A:79 , VAL A:81 , SER A:112 , PRO A:113 , GLY A:114 , ARG A:131 , TYR A:158 , ASN A:242 , PHE A:245 , GLY A:276 , ASP A:277 , PRO A:293 , LEU A:294 , ALA A:295 , CAJ A:503 , HOH A:603 , HOH A:611 , HOH A:618 , HOH A:620 , HOH A:626 , HOH A:628 , HOH A:648 , HOH A:668 , HOH A:679 , TYR B:419 , ALA B:420 , PRO B:421	BINDING SITE FOR RESIDUE FAD A 501
2	AC2	SOFTWARE	HOH A:688 , MG B:502 , HOH B:713 , HOH B:715	BINDING SITE FOR RESIDUE MG A 502
3	AC3	SOFTWARE	ALA A:11 , THR A:15 , SER A:18 , GLN A:19 , ARG A:22 , SER A:39 , ALA A:41 , ASN A:42 , CYS A:43 , LYS A:71 , ALA A:295 , HIS A:299 , FAD A:501 , HOH A:601 , HOH A:698 , TYR B:361 , TYR B:419 , PRO B:426 , LYS B:427 , MET B:432 , TYR B:435	BINDING SITE FOR RESIDUE CAJ A 503
4	AC4	SOFTWARE	TYR A:419 , ALA A:420 , VAL B:7 , GLY B:8 , VAL B:10 , ALA B:11 , GLY B:12 , PHE B:32 , GLU B:33 , LYS B:34 , ASP B:35 , ASN B:42 , CYS B:43 , HIS B:79 , GLU B:80 , VAL B:81 , SER B:112 , PRO B:113 , GLY B:114 , ARG B:131 , TYR B:158 , ASN B:242 , PHE B:245 , GLY B:276 , ASP B:277 , PRO B:293 , LEU B:294 , ALA B:295 , CAJ B:504 , HOH B:601 , HOH B:605 , HOH B:609 , HOH B:613 , HOH B:628 , HOH B:654 , HOH B:657	BINDING SITE FOR RESIDUE FAD B 501
5	AC5	SOFTWARE	ILE A:84 , ASN A:85 , ASP A:86 , MG A:502 , HOH A:688	BINDING SITE FOR RESIDUE MG B 502
6	AC6	SOFTWARE	HOH B:704	BINDING SITE FOR RESIDUE CL B 503
7	AC7	SOFTWARE	TYR A:419 , PRO A:426 , LYS A:427 , MET A:432 , TYR A:435 , VAL B:10 , ALA B:11 , ALA B:14 , THR B:15 , SER B:18 , GLN B:19 , ARG B:22 , SER B:39 , PHE B:40 , ALA B:41 , ASN B:42 , CYS B:43 , LYS B:71 , ALA B:295 , HIS B:299 , FAD B:501	BINDING SITE FOR RESIDUE CAJ B 504

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

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:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh....eeee........hhhhhhhhhh....hhhhhh..hhhhhhhhhh.eee..eeeeeee....eeeeee....eeeeee..eeee...eee.........ee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh..eee...eeeee..eeee....eee..eeee...eee.hhhhh...........ee...........eee....eeee......ee...hhhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhh.eeeeeeeee..........eeeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhhh............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4emw A   2 PKIVVVGAVAGGATCASQIRRLDKESDIIIFEKDRDMSFANCALPYVIGEVVEDRRYALAYTPEKFYDRKQITVKTYHEVIAINDERQTVSVLNRKTNEQFEESYDKLILSPGASANSLGFESDITFTLRNLEDTDAIDQFIKANQVDKVLVVGAGYVSLEVLENLYERGLHPTLIHRSDKINKLMDADMNQPILDELDKREIPYRLNEEINAINGNEITFKSGKVEHYDMIIEGVGTHPNSKFIESSNIKLDRKGFIPVNDKFETNVPNIYAIGDIATSHYRHVDLPASVPLAWGAHRAASIVAEQIAGNDTIEFKGFLGNNIVKFFDYTFASVGVKPNELKQFDYKMVEVTQGAHANYYPGNSPLHLRVYYDTSNRQILRAAAVGKEGADKRIDVLSMAMMNQLTVDELTEFEVAYAPPYSHPKDLINMIGYKA 437
                                    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       361       371       381       391       401       411       421       431

Chain B from PDB  Type:PROTEIN  Length:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh....eeee........hhhhhhhhhh....hhhhh...hhhhhhhhhh.eee..eeeeeee....eeeeee....eeeeee..eeee...eee.........ee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh...eee...eeeee..eeee....eee..eeee...eee.hhhhh...........ee...........eee....eeee......ee...hhhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhh.eeeeeeeee..........eeeeeeeee.....eeeeeeee..hhhhhhhhhhhhhhh...hhhhhhh............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4emw B   2 PKIVVVGAVAGGATCASQIRRLDKESDIIIFEKDRDMSFANCALPYVIGEVVEDRRYALAYTPEKFYDRKQITVKTYHEVIAINDERQTVSVLNRKTNEQFEESYDKLILSPGASANSLGFESDITFTLRNLEDTDAIDQFIKANQVDKVLVVGAGYVSLEVLENLYERGLHPTLIHRSDKINKLMDADMNQPILDELDKREIPYRLNEEINAINGNEITFKSGKVEHYDMIIEGVGTHPNSKFIESSNIKLDRKGFIPVNDKFETNVPNIYAIGDIATSHYRHVDLPASVPLAWGAHRAASIVAEQIAGNDTIEFKGFLGNNIVKFFDYTFASVGVKPNELKQFDYKMVEVTQGAHANYYPGNSPLHLRVYYDTSNRQILRAAAVGKEGADKRIDVLSMAMMNQLTVDELTEFEVAYAPPYSHPKDLINMIGYKA 437
                                    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       361       371       381       391       401       411       421       431

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

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
		CAJ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4emw)

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4emw
		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
	CDR_STAA3 \| Q2FIA5
		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)
	1.8.1.14
		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

Analysis Tools

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
	CDR_STAA3 \| Q2FIA5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description