4HUR - JenaLib

Title :   CRYSTAL STRUCTURE OF STREPTOGRAMIN GROUP A ANTIBIOTIC ACETYLTRANSFERASE VATA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH ACETYL COENZYME A

Authors :   P. J. Stogios, G. Minasov, E. Evdokimova, Z. Wawrzak, V. Yim, M. Krishna R. Di Leo, P. Courvalin, A. Savchenko, W. F. Anderson, Center For St Genomics Of Infectious Diseases (Csgid)

Date :   03 Nov 12 (Deposition) - 14 Nov 12 (Release) - 24 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Structural Genomics, Antibiotic Resistance, Center For Structural Genomics Of Infectious Diseases (Csgid), Niaid, National Institute Of Allergy And Infectious Diseases, Xenobiotic Acyltransferase (Xat) Family, Hexapeptide Repeat Acyltransferase, Streptogramin Group A Antibiotic Acetyltransferase, Streptogramin Group A Antibiotics, Streptogramin A, Virginiamycin M1, Dalfopristin, Acetyl Coenzyme A, Coenzyme A, Intracellular, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Stogios, M. L. Kuhn, E. Evdokimova, P. Courvalin, W. F. Anderson, A. Savchenko
Potential For Reduction Of Streptogramin A Resistance Revealed By Structural Analysis Of Acetyltransferase Vata.
Antimicrob. Agents Chemother. V. 58 7083 2014
PubMed-ID: 25223995 | Reference-DOI: 10.1128/AAC.03743-14

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 36)

Sites (36, 36)

Asymmetric Unit (36, 36)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:42 , SER A:73 , ILE A:74 , GLY A:75 , TRP A:126 , GLY A:128 , ARG A:129 , ALA A:146 , ALA A:147 , GLY A:162 , GLY A:163 , ILE A:169 , ARG A:170 , HOH A:402 , HOH A:472 , HOH A:550 , HOH A:575 , TYR B:57 , ALA B:85 , ASN B:86 , HIS B:87 , LYS B:116 , THR B:152 , PRO B:165 , HOH B:405 , HOH B:463	BINDING SITE FOR RESIDUE ACO A 301
02	AC2	SOFTWARE	LYS A:27 , GLY A:38 , GLU A:39 , ARG A:70 , HOH A:432 , HOH A:446	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	LYS A:153 , LYS A:167 , PHE A:168	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	ARG A:88 , ASP A:112 , ASN C:203	BINDING SITE FOR RESIDUE SO4 A 304
05	AC5	SOFTWARE	TYR A:59 , GLU A:60 , HOH A:454	BINDING SITE FOR RESIDUE EDO A 305
06	AC6	SOFTWARE	LYS A:153 , ASN A:154	BINDING SITE FOR RESIDUE EDO A 306
07	AC7	SOFTWARE	ASN A:123 , TRP A:187 , ASN A:188 , HOH A:537	BINDING SITE FOR RESIDUE EDO A 307
08	AC8	SOFTWARE	GLU A:39 , TYR A:40 , ARG A:70 , TRP A:187 , LEU A:189 , MET A:191	BINDING SITE FOR RESIDUE EDO A 308
09	AC9	SOFTWARE	ILE A:193 , ASN A:197 , LYS A:212 , LEU A:216	BINDING SITE FOR RESIDUE EDO A 309
10	BC1	SOFTWARE	GLY A:140 , ASN A:154 , VAL A:155 , ALA A:156 , PRO A:157 , HOH A:500	BINDING SITE FOR RESIDUE EDO A 310
11	BC2	SOFTWARE	ARG A:211 , HOH A:508 , HOH A:566 , LYS B:27 , HOH B:420	BINDING SITE FOR RESIDUE EDO A 311
12	BC3	SOFTWARE	GLU A:120 , GLY A:122 , ILE A:139 , HOH A:420 , HOH A:500	BINDING SITE FOR RESIDUE EDO A 312
13	BC4	SOFTWARE	ARG A:129 , HOH A:585 , ASP B:53 , GLN B:54	BINDING SITE FOR RESIDUE EDO A 313
14	BC5	SOFTWARE	GLY A:117 , ASP A:118 , LYS A:138	BINDING SITE FOR RESIDUE EDO A 314
15	BC6	SOFTWARE	LYS A:138	BINDING SITE FOR RESIDUE EDO A 315
16	BC7	SOFTWARE	ASN A:164 , HOH A:426 , ASN B:164 , HOH B:502 , ASN C:164 , HOH C:422	BINDING SITE FOR RESIDUE NA A 316
17	BC8	SOFTWARE	TYR B:42 , SER B:73 , ILE B:74 , GLY B:75 , TRP B:126 , ILE B:127 , GLY B:128 , ARG B:129 , ALA B:146 , ALA B:147 , GLY B:162 , GLY B:163 , ILE B:169 , ARG B:170 , HOH B:408 , HOH B:466 , HOH B:496 , HOH B:511 , TYR C:57 , ALA C:85 , ASN C:86 , HIS C:87 , LYS C:116 , MET C:134 , THR C:152 , PRO C:165 , HOH C:429 , HOH C:466	BINDING SITE FOR RESIDUE ACO B 301
18	BC9	SOFTWARE	HOH A:583 , GLU B:39 , ARG B:70 , TRP B:187 , LEU B:189 , MET B:191 , ILE B:194 , HOH B:564	BINDING SITE FOR RESIDUE EDO B 302
19	CC1	SOFTWARE	MET A:208 , LEU B:36 , GLY B:38 , ILE B:67 , ILE B:68 , GLY B:69 , HOH B:409 , HOH B:462	BINDING SITE FOR RESIDUE EDO B 303
20	CC2	SOFTWARE	ASN A:203 , ARG B:88 , LEU B:189 , ASP B:190 , ILE B:193 , HOH B:460	BINDING SITE FOR RESIDUE EDO B 304
21	CC3	SOFTWARE	PRO B:9 , ASP B:10 , HOH B:562	BINDING SITE FOR RESIDUE EDO B 305
22	CC4	SOFTWARE	LYS B:153 , LYS B:167 , PHE B:168	BINDING SITE FOR RESIDUE EDO B 306
23	CC5	SOFTWARE	VAL B:155	BINDING SITE FOR RESIDUE EDO B 307
24	CC6	SOFTWARE	GLY B:117 , ASP B:118 , LYS B:138 , HOH B:597	BINDING SITE FOR RESIDUE CL B 308
25	CC7	SOFTWARE	HOH A:593 , TYR B:57 , HOH B:520	BINDING SITE FOR RESIDUE CL B 309
26	CC8	SOFTWARE	TYR A:57 , ALA A:85 , ASN A:86 , LYS A:116 , MET A:134 , THR A:152 , PRO A:165 , HOH A:538 , TYR C:42 , SER C:73 , ILE C:74 , GLY C:75 , TRP C:126 , ILE C:127 , GLY C:128 , ARG C:129 , ALA C:146 , ALA C:147 , GLY C:162 , GLY C:163 , ILE C:169 , ARG C:170 , HOH C:401 , HOH C:443 , HOH C:460 , HOH C:561	BINDING SITE FOR RESIDUE ACO C 301
27	CC9	SOFTWARE	LYS C:27 , GLY C:38 , GLU C:39 , ARG C:70 , HOH C:456 , HOH C:533 , HOH C:548	BINDING SITE FOR RESIDUE SO4 C 302
28	DC1	SOFTWARE	LYS C:167 , PHE C:168	BINDING SITE FOR RESIDUE EDO C 303
29	DC2	SOFTWARE	ILE C:30 , THR C:31 , ASN C:32 , HOH C:600	BINDING SITE FOR RESIDUE EDO C 304
30	DC3	SOFTWARE	GLU C:120 , GLY C:122 , ILE C:139 , GLY C:140	BINDING SITE FOR RESIDUE EDO C 305
31	DC4	SOFTWARE	SER C:109 , LEU C:110 , LYS C:111 , HOH C:612	BINDING SITE FOR RESIDUE EDO C 306
32	DC5	SOFTWARE	GLU C:33 , ASN C:34 , LEU C:36 , VAL C:61 , LYS C:65	BINDING SITE FOR RESIDUE EDO C 307
33	DC6	SOFTWARE	ASN C:123 , GLN C:185 , TRP C:187 , ASN C:188	BINDING SITE FOR RESIDUE EDO C 308
34	DC7	SOFTWARE	ASN B:203 , ARG C:88 , HOH C:557	BINDING SITE FOR RESIDUE EDO C 309
35	DC8	SOFTWARE	HOH B:511 , PRO C:95 , HIS C:97 , HOH C:442	BINDING SITE FOR RESIDUE EDO C 310
36	DC9	SOFTWARE	ARG B:129 , ASP C:53 , GLN C:54 , THR C:79 , HOH C:415	BINDING SITE FOR RESIDUE EDO C 311

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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:211
                                                                                                                                                                                                                                                   
               SCOP domains d4hura_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhh....eee....eee.....hhhh.ee.........eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hur A   7 HGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLD 217
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216

Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4hurb_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhh....eee....eee.....hhhh.ee.........eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hur B   7 HGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLD 217
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216

Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d4hurc_ C: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eee.hhhh....eee....eee.....hhhh.ee.........eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hur C   6 DHGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKL 215
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215

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 (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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
		ACO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ 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 ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]
		DC4	[ RasMol ]	+environment [ RasMol ]
		DC5	[ RasMol ]	+environment [ RasMol ]
		DC6	[ RasMol ]	+environment [ RasMol ]
		DC7	[ RasMol ]	+environment [ RasMol ]
		DC8	[ RasMol ]	+environment [ RasMol ]
		DC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:164 - Pro A:165	[ RasMol ]
		Asn B:164 - Pro B:165	[ RasMol ]
		Asn C:164 - Pro C:165	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4hur
		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
	VATA_STAAU \| P26839
		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)
	2.3.1.-
		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

Description