PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4HUS
Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (230 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF STREPTOGRAMIN GROUP A ANTIBIOTIC ACETYLTRANSFERASE VATA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH VIRGINIAMYCIN M1
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) - 21 Nov 12 (Release) - 24 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
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-Antibiotic Complex
(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
[
close entry info
]
Hetero Components
(7, 40)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
3a: SODIUM ION (NAa)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
7a: VIRGINIAMYCIN M1 (VIRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
9
Ligand/Ion
CHLORIDE ION
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
NA
1
Ligand/Ion
SODIUM ION
4
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
6
SO4
8
Ligand/Ion
SULFATE ION
7
VIR
1
Ligand/Ion
VIRGINIAMYCIN M1
[
close Hetero Component info
]
Sites
(40, 40)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:70 , LEU A:189 , MET A:191 , HOH A:503
BINDING SITE FOR RESIDUE SO4 A 301
02
AC2
SOFTWARE
ASN A:203 , ARG C:88 , ASP C:112 , EDO C:307
BINDING SITE FOR RESIDUE SO4 A 302
03
AC3
SOFTWARE
LYS A:153 , LEU A:166 , LYS A:167 , PHE A:168 , HOH A:478
BINDING SITE FOR RESIDUE SO4 A 303
04
AC4
SOFTWARE
ASN A:164 , HOH A:422 , ASN B:164 , HOH B:417 , ASN C:164 , HOH C:514
BINDING SITE FOR RESIDUE NA A 304
05
AC5
SOFTWARE
GLY A:117 , ASP A:118 , LYS A:138
BINDING SITE FOR RESIDUE CL A 305
06
AC6
SOFTWARE
ARG A:100 , HOH A:518
BINDING SITE FOR RESIDUE CL A 306
07
AC7
SOFTWARE
LYS A:171
BINDING SITE FOR RESIDUE CL A 307
08
AC8
SOFTWARE
GLU A:60
BINDING SITE FOR RESIDUE CL A 308
09
AC9
SOFTWARE
GLY A:84 , LEU A:216
BINDING SITE FOR RESIDUE EDO A 309
10
BC1
SOFTWARE
LYS A:46 , ARG A:47
BINDING SITE FOR RESIDUE EDO A 310
11
BC2
SOFTWARE
ASP A:53 , THR A:79 , HOH A:420 , HOH A:532 , CL B:306
BINDING SITE FOR RESIDUE EDO A 311
12
BC3
SOFTWARE
LYS A:138 , GLY A:140 , VAL A:155 , HOH A:562
BINDING SITE FOR RESIDUE EDO A 312
13
BC4
SOFTWARE
GLU A:12 , LYS A:27 , PRO A:28 , HOH A:522 , ARG B:211
BINDING SITE FOR RESIDUE PEG A 313
14
BC5
SOFTWARE
PRO A:76 , GLY A:128 , ARG A:129 , ALA A:146 , ALA A:147 , HOH A:410 , TYR C:57 , HOH C:511
BINDING SITE FOR RESIDUE PEG A 314
15
BC6
SOFTWARE
ALA A:146 , HOH A:454
BINDING SITE FOR RESIDUE PEG A 315
16
BC7
SOFTWARE
ASN A:20 , LEU A:23 , TYR A:42 , ASP A:44 , HOH A:410 , HOH A:412 , HOH A:488 , HOH A:588 , TYR C:59 , GLY C:84 , ASN C:86 , HIS C:87 , HIS C:97 , LEU C:98 , PRO C:108 , LEU C:113 , HOH C:571
BINDING SITE FOR RESIDUE VIR A 316
17
BC8
SOFTWARE
LYS B:153 , LEU B:166 , LYS B:167 , PHE B:168 , HOH B:553
BINDING SITE FOR RESIDUE SO4 B 301
18
BC9
SOFTWARE
LYS B:27 , GLY B:38 , GLU B:39 , ARG B:70 , HOH B:449
BINDING SITE FOR RESIDUE SO4 B 302
19
CC1
SOFTWARE
ARG B:88 , ASN C:203
BINDING SITE FOR RESIDUE SO4 B 303
20
CC2
SOFTWARE
ILE B:139
BINDING SITE FOR RESIDUE CL B 304
21
CC3
SOFTWARE
SER B:174 , GLY B:176
BINDING SITE FOR RESIDUE CL B 305
22
CC4
SOFTWARE
EDO A:311 , LYS B:46 , ARG B:47
BINDING SITE FOR RESIDUE CL B 306
23
CC5
SOFTWARE
LYS B:214 , HOH B:527
BINDING SITE FOR RESIDUE EDO B 307
24
CC6
SOFTWARE
TRP B:126 , GLY B:128 , ALA B:146 , ALA B:147 , PEG B:312 , PGE B:314 , HOH B:471
BINDING SITE FOR RESIDUE EDO B 308
25
CC7
SOFTWARE
ASN B:154 , HOH B:531
BINDING SITE FOR RESIDUE EDO B 309
26
CC8
SOFTWARE
GLU B:39 , ARG B:70 , LEU B:189 , MET B:191
BINDING SITE FOR RESIDUE EDO B 310
27
CC9
SOFTWARE
TYR B:57 , TYR B:59
BINDING SITE FOR RESIDUE EDO B 311
28
DC1
SOFTWARE
ALA B:146 , EDO B:308 , HOH B:537
BINDING SITE FOR RESIDUE PEG B 312
29
DC2
SOFTWARE
HIS B:87 , LEU B:98 , TYR C:42 , ASP C:44 , HOH C:506 , HOH C:529 , HOH C:632
BINDING SITE FOR RESIDUE PGE B 313
30
DC3
SOFTWARE
TYR A:57 , HIS A:87 , HOH A:476 , TYR B:42 , ASP B:44 , GLY B:75 , TRP B:126 , ILE B:127 , ARG B:129 , EDO B:308 , HOH B:471
BINDING SITE FOR RESIDUE PGE B 314
31
DC4
SOFTWARE
LYS C:27 , GLU C:39 , ARG C:70 , HOH C:579
BINDING SITE FOR RESIDUE SO4 C 301
32
DC5
SOFTWARE
LYS C:153 , LYS C:167 , PHE C:168 , HOH C:615
BINDING SITE FOR RESIDUE SO4 C 302
33
DC6
SOFTWARE
ARG C:47
BINDING SITE FOR RESIDUE CL C 303
34
DC7
SOFTWARE
ARG C:100
BINDING SITE FOR RESIDUE CL C 304
35
DC8
SOFTWARE
ALA C:146 , ILE C:160
BINDING SITE FOR RESIDUE EDO C 305
36
DC9
SOFTWARE
ASN C:13 , ILE C:14
BINDING SITE FOR RESIDUE EDO C 306
37
EC1
SOFTWARE
PRO A:199 , SO4 A:302 , MET C:107
BINDING SITE FOR RESIDUE EDO C 307
38
EC2
SOFTWARE
LYS C:111 , GLN C:185 , ASN C:188 , HOH C:604
BINDING SITE FOR RESIDUE EDO C 308
39
EC3
SOFTWARE
ASP C:10 , PRO C:11 , GLU C:39 , HOH C:611
BINDING SITE FOR RESIDUE EDO C 309
40
EC4
SOFTWARE
GLU C:33 , ASN C:34 , GLU C:60
BINDING SITE FOR RESIDUE EDO C 310
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d4husa_ (A:)
1b: SCOP_d4husb_ (B:)
1c: SCOP_d4husc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Single-stranded left-handed beta-helix
(154)
Superfamily
:
Trimeric LpxA-like enzymes
(147)
Family
:
Galactoside acetyltransferase-like
(21)
Protein domain
:
automated matches
(6)
Staphylococcus aureus [TaxId: 1280]
(3)
1a
d4husa_
A:
1b
d4husb_
B:
1c
d4husc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (238 KB)
Header - Asym.Unit
Biol.Unit 1 (230 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4HUS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help