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.
5FYU
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (86 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 THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 3-AMINO-4-METHYL-1,3-DIHYDRO-2H-INDOL-2-ONE (N10042A)
Authors
:
R. Nowak, T. Krojer, C. Johansson, N. Pearce, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsm C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brennan, U. Oppermann
Date
:
09 Mar 16 (Deposition) - 23 Mar 16 (Release) - 23 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.06
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Jarid1B, Plu1, Pandda, Fragment Soaking, X-Ray Fragment Screening, Structural Genomics Consortium, Sgc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Crystal Structure Of The Catalytic Domain Of Human Jarid1B In Complex With N10042A
To Be Published
[
close entry info
]
Hetero Components
(7, 22)
Info
All Hetero Components
1a: (3R)-3-AZANYL-4-METHYL-1,3-DIHYDRO... (BY4a)
2a: CHLORIDE ION (CLa)
3a: DIMETHYL SULFOXIDE (DMSa)
3b: DIMETHYL SULFOXIDE (DMSb)
3c: DIMETHYL SULFOXIDE (DMSc)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
4i: 1,2-ETHANEDIOL (EDOi)
4j: 1,2-ETHANEDIOL (EDOj)
4k: 1,2-ETHANEDIOL (EDOk)
4l: 1,2-ETHANEDIOL (EDOl)
4m: 1,2-ETHANEDIOL (EDOm)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
6a: PHOSPHATE ION (PO4a)
7a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BY4
1
Ligand/Ion
(3R)-3-AZANYL-4-METHYL-1,3-DIHYDROINDOL-2-ONE
2
CL
1
Ligand/Ion
CHLORIDE ION
3
DMS
3
Ligand/Ion
DIMETHYL SULFOXIDE
4
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
5
MN
2
Ligand/Ion
MANGANESE (II) ION
6
PO4
1
Ligand/Ion
PHOSPHATE ION
7
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:692 , CYS A:695 , CYS A:715 , HIS A:718
BINDING SITE FOR RESIDUE ZN A1755
02
AC2
SOFTWARE
HIS A:499 , GLU A:501 , HIS A:587 , HOH A:2114 , HOH A:2115 , HOH A:2122
BINDING SITE FOR RESIDUE MN A1756
03
AC3
SOFTWARE
HIS A:399
BINDING SITE FOR RESIDUE MN A1757
04
AC4
SOFTWARE
HIS A:622 , LYS A:694 , HIS A:718 , HOH A:2157 , HOH A:2235
BINDING SITE FOR RESIDUE PO4 A1758
05
AC5
SOFTWARE
ASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , EDO A:1762 , HOH A:2169
BINDING SITE FOR RESIDUE EDO A1759
06
AC6
SOFTWARE
PHE A:83 , GLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , VAL A:489 , HOH A:2086
BINDING SITE FOR RESIDUE EDO A1760
07
AC7
SOFTWARE
ARG A:666 , TYR A:734 , THR A:737
BINDING SITE FOR RESIDUE EDO A1761
08
AC8
SOFTWARE
ARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , EDO A:1759 , HOH A:2160
BINDING SITE FOR RESIDUE EDO A1762
09
AC9
SOFTWARE
PRO A:30 , VAL A:568
BINDING SITE FOR RESIDUE EDO A1763
10
BC1
SOFTWARE
ASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:713
BINDING SITE FOR RESIDUE EDO A1764
11
BC2
SOFTWARE
GLY A:524 , ARG A:584 , HOH A:2239
BINDING SITE FOR RESIDUE EDO A1765
12
BC3
SOFTWARE
ARG A:670 , VAL A:674 , ILE A:675 , HOH A:2082 , HOH A:2186
BINDING SITE FOR RESIDUE EDO A1766
13
BC4
SOFTWARE
HIS A:564 , GLU A:565
BINDING SITE FOR RESIDUE EDO A1767
14
BC5
SOFTWARE
ARG A:98 , CYS A:497 , HIS A:499 , EDO A:1769 , BY4 A:1774 , HOH A:2048 , HOH A:2049
BINDING SITE FOR RESIDUE EDO A1768
15
BC6
SOFTWARE
GLN A:88 , GLN A:96 , THR A:97 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , EDO A:1768
BINDING SITE FOR RESIDUE EDO A1769
16
BC7
SOFTWARE
LEU A:101 , GLY A:481 , ASP A:502 , ASN A:601 , DMS A:1771 , HOH A:2047 , HOH A:2123
BINDING SITE FOR RESIDUE EDO A1770
17
BC8
SOFTWARE
TRP A:486 , TYR A:488 , ALA A:599 , VAL A:600 , ASN A:601 , EDO A:1770
BINDING SITE FOR RESIDUE DMS A1771
18
BC9
SOFTWARE
GLU A:631 , LYS A:635 , GLU A:683 , PHE A:700 , ARG A:735 , TYR A:736
BINDING SITE FOR RESIDUE DMS A1772
19
CC1
SOFTWARE
TRP A:504 , GLU A:531 , HIS A:617 , LEU A:621 , HOH A:2120 , HOH A:2139 , HOH A:2241
BINDING SITE FOR RESIDUE DMS A1773
20
CC2
SOFTWARE
TYR A:425 , TYR A:488 , PHE A:496 , ASN A:509 , LYS A:517 , EDO A:1768 , HOH A:2085
BINDING SITE FOR RESIDUE BY4 A1774
21
CC3
SOFTWARE
LEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419
BINDING SITE FOR RESIDUE CL A1775
[
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
(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 A
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 (93 KB)
Header - Asym.Unit
Biol.Unit 1 (86 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
5FYU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help