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...
Getting 'PROSITE' information from database.
2YC0
Biol. Unit 1
Info
Asym.Unit (66 KB)
Biol.Unit 1 (119 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE
Authors
:
R. Chowdhury, I. J. Clifton, C. J. Schofield
Date
:
10 Mar 11 (Deposition) - 30 Mar 11 (Release) - 11 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Oxidoreductase, Dioxygenase, Metal-Binding, Transcription, Helix- Loop-Helix-Beta, Dsbh, Facial Triad, Asparaginyl/Aspartyl Hydroxylase, Transcription And Epigenetic Regulation, Signaling, Development, Cell Structure, Ankyrin Repeat Domain, Ard, Beta- Hydroxylation, Transcription Activator/Inhibitor, Phosphorylation, S-Nitrosylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Chowdhury, K. K. Yeoh, Y. M. Tian, L. Hillringhaus, E. A. Bagg, N. R. Rose, I. K. Leung, X. S. Li, E. C. Woon, M. Yang, M. A. Mcdonough, O. N. King, I. J. Clifton, R. J. Klose, T. D. Claridge, P. J. Ratcliffe, C. J. Schofield, A. Kawamura
The Oncometabolite 2-Hydroxyglutarate Inhibits Histone Lysine Demethylases.
Embo Rep. V. 12 463 2011
[
close entry info
]
Hetero Components
(4, 18)
Info
All Hetero Components
1a: (2R)-2-HYDROXYPENTANEDIOIC ACID (2HGa)
2a: FE (II) ION (FE2a)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2HG
2
Ligand/Ion
(2R)-2-HYDROXYPENTANEDIOIC ACID
2
FE2
2
Ligand/Ion
FE (II) ION
3
GOL
6
Ligand/Ion
GLYCEROL
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:199 , ASP A:201 , HIS A:279 , 2HG A:601 , GOL A:604
BINDING SITE FOR RESIDUE FE2 A 501
2
AC2
SOFTWARE
TYR A:145 , THR A:196 , HIS A:199 , ASP A:201 , ASN A:205 , PHE A:207 , LYS A:214 , HIS A:279 , ILE A:281 , ASN A:294 , TRP A:296 , FE2 A:501 , GOL A:604
BINDING SITE FOR RESIDUE 2HG A 601
3
AC3
SOFTWARE
LYS A:99 , LEU A:101 , TYR A:230 , SER A:240 , GLN A:241 , ASP A:243 , HOH A:2091
BINDING SITE FOR RESIDUE GOL A 602
4
AC4
SOFTWARE
ASP A:222 , LYS A:315 , MET A:319
BINDING SITE FOR RESIDUE GOL A 603
5
AC5
SOFTWARE
TYR A:102 , GLN A:147 , THR A:196 , HIS A:199 , ASP A:201 , TRP A:296 , FE2 A:501 , 2HG A:601
BINDING SITE FOR RESIDUE GOL A 604
6
AC6
SOFTWARE
ASP A:222 , LYS A:311 , ALA A:312 , HOH A:2092 , HOH A:2093
BINDING SITE FOR RESIDUE SO4 A 901
7
AC7
SOFTWARE
ARG A:138 , GLY A:140 , GLU A:141 , GLU A:142
BINDING SITE FOR RESIDUE SO4 A 902
8
AC8
SOFTWARE
ARG A:120
BINDING SITE FOR RESIDUE SO4 A 904
9
AC9
SOFTWARE
ARG A:143 , GLU A:192 , GLY A:193 , LEU A:285 , ASN A:286
BINDING SITE FOR RESIDUE SO4 A 905
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_051028 (P41A, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051028
P
41
A
HIF1N_HUMAN
Polymorphism
2295778
A
P
41
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: JMJC (A:142-312)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
JMJC
PS51184
JmjC domain profile.
HIF1N_HUMAN
142-312
2
A:142-312
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2yc0a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Clavaminate synthase-like
(197)
Family
:
Hypoxia-inducible factor HIF ihhibitor (FIH1)
(26)
Protein domain
:
Hypoxia-inducible factor HIF ihhibitor (FIH1)
(26)
Human (Homo sapiens) [TaxId: 9606]
(26)
1a
d2yc0a_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Cupin_8_2yc0A01 (A:48-302)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cupin
(179)
Family
:
Cupin_8
(14)
Homo sapiens (Human)
(14)
1a
Cupin_8-2yc0A01
A:48-302
[
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
Asymmetric Unit 2
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 (66 KB)
Header - Asym.Unit
Biol.Unit 1 (119 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
2YC0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help