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.
2Y0C
Biol. Unit 2
Info
Asym.Unit (629 KB)
Biol.Unit 1 (311 KB)
Biol.Unit 2 (314 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BCEC MUTATION Y10S
Authors
:
J. Rocha, A. O. Popescu, P. Borges, D. Mil-Homens, I. Sa-Correia, A. M. F C. Frazao
Date
:
02 Dec 10 (Deposition) - 27 Jul 11 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, Carbohydrate Synthesis, Exopolysaccharide, Cystic Fibrosis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Rocha, A. O. Popescu, P. Borges, D. Mil-Homens, L. M. Moreira, I. Sa-Correia, A. M. Fialho, C. Frazao
Structure Of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec And Role Of Tyr10 In Final Hydrolysis Of Ugd Thioester Intermediate.
J. Bacteriol. V. 193 3978 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
5a: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAa)
5b: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAb)
5c: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAc)
5d: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ... (UGAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
SO4
5
Ligand/Ion
SULFATE ION
4
TRS
-1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5
UGA
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
15: CC9 (SOFTWARE)
16: DC1 (SOFTWARE)
17: DC2 (SOFTWARE)
18: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ARG A:246 , ARG A:247 , HIS C:199
BINDING SITE FOR RESIDUE SO4 A 512
02
AC4
SOFTWARE
ARG A:185 , LYS A:189 , TYR A:204 , ARG D:185 , GLU D:186 , LYS D:189
BINDING SITE FOR RESIDUE SO4 A 513
03
BC2
SOFTWARE
HIS B:258 , TYR B:261 , ARG D:167 , ASN D:198
BINDING SITE FOR RESIDUE SO4 B 511
04
BC4
SOFTWARE
ARG B:355 , HOH B:2229 , HIS C:378 , PRO C:379 , SER C:380
BINDING SITE FOR RESIDUE SO4 B 513
05
BC5
SOFTWARE
ARG B:185 , GLU B:186 , LYS B:189 , ARG C:185 , LYS C:189
BINDING SITE FOR RESIDUE SO4 B 514
06
BC9
SOFTWARE
GLU C:154 , PHE C:155 , LEU C:156 , GLU C:158 , LYS C:214 , ASN C:218 , ILE C:225 , PHE C:259 , LEU C:260 , TYR C:261 , GLY C:265 , TYR C:266 , GLY C:267 , CYS C:270 , PHE C:271 , PHE C:330 , LYS C:331 , ARG C:431 , HOH C:2046 , HOH C:2109 , HOH C:2131 , HOH C:2232 , HOH C:2264 , HOH C:2267 , HOH C:2268 , HOH C:2269 , ARG D:254
BINDING SITE FOR RESIDUE UGA C 501
07
CC1
SOFTWARE
HIS A:199 , ARG C:246 , ARG C:247 , HOH C:2270 , HOH C:2271
BINDING SITE FOR RESIDUE SO4 C 512
08
CC2
SOFTWARE
GLY C:112 , PHE C:113 , ARG C:183
BINDING SITE FOR RESIDUE SO4 C 513
09
CC3
SOFTWARE
PHE C:165 , PRO C:168 , ILE C:171 , PHE C:195 , HOH C:2085 , HOH C:2272
BINDING SITE FOR RESIDUE ACT C 521
10
CC4
SOFTWARE
ARG C:246 , TYR C:257 , HIS C:258 , PHE C:259 , TYR C:261 , HOH C:2273
BINDING SITE FOR RESIDUE GOL C 531
11
CC5
SOFTWARE
ARG C:254 , GLU D:154 , PHE D:155 , LEU D:156 , GLU D:158 , LYS D:214 , ASN D:218 , ILE D:225 , PHE D:259 , LEU D:260 , TYR D:261 , GLY D:265 , TYR D:266 , GLY D:267 , CYS D:270 , PHE D:271 , PHE D:330 , LYS D:331 , ARG D:431 , GOL D:532 , HOH D:2207 , HOH D:2236 , HOH D:2339 , HOH D:2374 , HOH D:2375 , HOH D:2376 , HOH D:2377
BINDING SITE FOR RESIDUE UGA D 501
12
CC6
SOFTWARE
ASN B:198 , HIS D:258 , TYR D:261 , HOH D:2378
BINDING SITE FOR RESIDUE SO4 D 511
13
CC7
SOFTWARE
ARG D:338 , ARG D:343
BINDING SITE FOR RESIDUE SO4 D 512
14
CC8
SOFTWARE
LYS A:140 , GLY D:443 , ARG D:455 , GLN D:456
BINDING SITE FOR RESIDUE SO4 D 513
15
CC9
SOFTWARE
PHE D:165 , PRO D:168 , PHE D:195 , HOH D:2169 , HOH D:2379
BINDING SITE FOR RESIDUE ACT D 521
16
DC1
SOFTWARE
PRO D:123 , VAL D:124 , TYR D:215 , THR D:281 , HOH D:2380
BINDING SITE FOR RESIDUE ACT D 522
17
DC2
SOFTWARE
PHE D:113 , MET D:146 , ARG D:183
BINDING SITE FOR RESIDUE GOL D 531
18
DC3
SOFTWARE
SER D:10 , GLU D:48 , GLU D:154 , LEU D:156 , ALA D:161 , UGA D:501 , HOH D:2032 , HOH D:2381
BINDING SITE FOR RESIDUE GOL D 532
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 C
Chain D
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 (629 KB)
Header - Asym.Unit
Biol.Unit 1 (311 KB)
Header - Biol.Unit 1
Biol.Unit 2 (314 KB)
Header - Biol.Unit 2
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
2Y0C
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
