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.
PLEASE WAIT...
Getting 'Exon' information from database.
3H7W
Asym. Unit
Info
Asym.Unit (48 KB)
Biol.Unit 1 (43 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 HIGH AFFINITY HETERODIMER OF HIF2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS WITH THE ARTIFICIAL LIGAND THS017
Authors
:
J. M. Key, T. H. Scheuermann, P. C. Anderson, V. Daggett, K. H. Gardner
Date
:
28 Apr 09 (Deposition) - 12 Jan 10 (Release) - 12 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pas Domain, Heterodimer, Protein Ligand Complex. , Activator, Angiogenesis, Congenital Erythrocytosis, Developmental Protein, Differentiation, Disease Mutation, Dna-Binding, Hydroxylation, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Ubl Conjugation, Alternative Splicing, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Key, T. H. Scheuermann, P. C. Anderson, V. Daggett, K. H. Gardner
Principles Of Ligand Binding Within A Completely Buried Cavity In Hif2Alpha Pas-B
J. Am. Chem. Soc. V. 131 17647 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: 2-NITRO-N-(THIOPHEN-3-YLMETHYL)-4-... (018a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
018
1
Ligand/Ion
2-NITRO-N-(THIOPHEN-3-YLMETHYL)-4-(TRIFLUOROMETHYL)ANILINE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:248 , MET A:252 , ALA A:277 , TYR A:281 , MET A:289 , SER A:292 , HIS A:293 , VAL A:302 , SER A:304 , TYR A:307 , MET A:309 , THR A:321 , CYS A:339 , ASN A:341
BINDING SITE FOR RESIDUE 018 A 1
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024280 (R430Q, chain B, )
2: VAR_049537 (E435K, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024280
R
430
Q
ARNT_HUMAN
Polymorphism
2229175
B
R
430
Q
2
UniProt
VAR_049537
E
435
K
ARNT_HUMAN
Polymorphism
2229176
B
E
435
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PAS (-|A:249-300,-|B:368-419)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PAS
PS50112
PAS repeat profile.
EPAS1_HUMAN
92-147
249-300
1
-
A:249-300
ARNT_HUMAN
161-235
368-419
1
-
B:368-419
[
close PROSITE info
]
Exons
(8, 8)
Info
All Exons
Exon 1.10b (A:236-260 (gaps))
Exon 1.11 (A:260-296)
Exon 1.12b (A:296-345 (gaps))
Exon 1.13 (A:345-349)
Exon 2.15b (B:358-389)
Exon 2.16 (B:390-414)
Exon 2.17 (B:415-465)
Exon 2.18b (B:465-467)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.9/1.10b
02: Boundary 1.10b/1.11
03: Boundary 1.11/1.12b
04: Boundary 1.12b/1.13
05: Boundary 1.13/1.14
06: Boundary 2.13d/2.15b
07: Boundary 2.15b/2.16
08: Boundary 2.16/2.17
09: Boundary 2.17/2.18b
10: Boundary 2.18b/2.19c
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3a
ENST00000263734
3a
ENSE00001875413
chr2:
46524541-46525076
536
EPAS1_HUMAN
1-9
9
0
-
-
1.5b
ENST00000263734
5b
ENSE00000809792
chr2:
46574012-46574202
191
EPAS1_HUMAN
9-73
65
0
-
-
1.7c
ENST00000263734
7c
ENSE00000751537
chr2:
46583290-46583441
152
EPAS1_HUMAN
73-123
51
0
-
-
1.8
ENST00000263734
8
ENSE00000751539
chr2:
46583863-46583947
85
EPAS1_HUMAN
124-152
29
0
-
-
1.9
ENST00000263734
9
ENSE00000751542
chr2:
46587777-46587895
119
EPAS1_HUMAN
152-191
40
0
-
-
1.10b
ENST00000263734
10b
ENSE00002181725
chr2:
46588024-46588229
206
EPAS1_HUMAN
192-260
69
1
A:236-260 (gaps)
47
1.11
ENST00000263734
11
ENSE00000751546
chr2:
46596966-46597072
107
EPAS1_HUMAN
260-296
37
1
A:260-296
37
1.12b
ENST00000263734
12b
ENSE00000962618
chr2:
46602829-46602976
148
EPAS1_HUMAN
296-345
50
1
A:296-345 (gaps)
50
1.13
ENST00000263734
13
ENSE00000751550
chr2:
46603678-46603892
215
EPAS1_HUMAN
345-417
73
1
A:345-349
5
1.14
ENST00000263734
14
ENSE00000962619
chr2:
46605033-46605226
194
EPAS1_HUMAN
417-481
65
0
-
-
1.15b
ENST00000263734
15b
ENSE00000962620
chr2:
46605796-46605906
111
EPAS1_HUMAN
482-518
37
0
-
-
1.16b
ENST00000263734
16b
ENSE00000962621
chr2:
46607366-46607856
491
EPAS1_HUMAN
519-682
164
0
-
-
1.17b
ENST00000263734
17b
ENSE00000962622
chr2:
46608735-46608861
127
EPAS1_HUMAN
682-724
43
0
-
-
1.18
ENST00000263734
18
ENSE00000751568
chr2:
46609114-46609228
115
EPAS1_HUMAN
725-763
39
0
-
-
1.19b
ENST00000263734
19b
ENSE00000751570
chr2:
46609564-46609737
174
EPAS1_HUMAN
763-821
59
0
-
-
1.20c
ENST00000263734
20c
ENSE00001816384
chr2:
46611648-46613836
2189
EPAS1_HUMAN
821-870
50
0
-
-
2.1a
ENST00000358595
1a
ENSE00002062254
chr1:
150849244-150849019
226
ARNT_HUMAN
1-9
9
0
-
-
2.3
ENST00000358595
3
ENSE00001717520
chr1:
150830936-150830825
112
ARNT_HUMAN
9-46
38
0
-
-
2.5b
ENST00000358595
5b
ENSE00001071957
chr1:
150825282-150825238
45
ARNT_HUMAN
46-61
16
0
-
-
2.6
ENST00000358595
6
ENSE00000960027
chr1:
150818783-150818739
45
ARNT_HUMAN
61-76
16
0
-
-
2.7
ENST00000358595
7
ENSE00001263986
chr1:
150814944-150814900
45
ARNT_HUMAN
76-91
16
0
-
-
2.8b
ENST00000358595
8b
ENSE00000960029
chr1:
150812130-150811917
214
ARNT_HUMAN
91-162
72
0
-
-
2.9c
ENST00000358595
9c
ENSE00000960030
chr1:
150808969-150808756
214
ARNT_HUMAN
163-234
72
0
-
-
2.10b
ENST00000358595
10b
ENSE00000960031
chr1:
150807116-150807014
103
ARNT_HUMAN
234-268
35
0
-
-
2.11
ENST00000358595
11
ENSE00000960032
chr1:
150804875-150804810
66
ARNT_HUMAN
268-290
23
0
-
-
2.12a
ENST00000358595
12a
ENSE00000960033
chr1:
150804379-150804294
86
ARNT_HUMAN
290-319
30
0
-
-
2.13d
ENST00000358595
13d
ENSE00001417988
chr1:
150802456-150802380
77
ARNT_HUMAN
319-344
26
0
-
-
2.15b
ENST00000358595
15b
ENSE00001414390
chr1:
150801703-150801569
135
ARNT_HUMAN
345-389
45
1
B:358-389
32
2.16
ENST00000358595
16
ENSE00001186051
chr1:
150799093-150799019
75
ARNT_HUMAN
390-414
25
1
B:390-414
25
2.17
ENST00000358595
17
ENSE00001804030
chr1:
150795821-150795670
152
ARNT_HUMAN
415-465
51
1
B:415-465
51
2.18b
ENST00000358595
18b
ENSE00001044530
chr1:
150790506-150790396
111
ARNT_HUMAN
465-502
38
1
B:465-467
3
2.19c
ENST00000358595
19c
ENSE00001044549
chr1:
150789909-150789837
73
ARNT_HUMAN
502-526
25
0
-
-
2.20
ENST00000358595
20
ENSE00001044525
chr1:
150789678-150789558
121
ARNT_HUMAN
527-567
41
0
-
-
2.21
ENST00000358595
21
ENSE00001044520
chr1:
150789366-150789264
103
ARNT_HUMAN
567-601
35
0
-
-
2.22a
ENST00000358595
22a
ENSE00001044548
chr1:
150788882-150788735
148
ARNT_HUMAN
601-650
50
0
-
-
2.23a
ENST00000358595
23a
ENSE00001151505
chr1:
150786715-150786553
163
ARNT_HUMAN
651-705
55
0
-
-
2.24a
ENST00000358595
24a
ENSE00001371736
chr1:
150785814-150785648
167
ARNT_HUMAN
705-760
56
0
-
-
2.25f
ENST00000358595
25f
ENSE00001855735
chr1:
150784586-150782181
2406
ARNT_HUMAN
761-789
29
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3h7wb_ (B:)
2a: SCOP_d3h7wa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Profilin-like
(304)
Superfamily
:
PYP-like sensor domain (PAS domain)
(163)
Family
:
automated matches
(33)
Protein domain
:
automated matches
(33)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3h7wb_
B:
Family
:
Hypoxia-inducible factor Hif2a, C-terminal domain
(10)
Protein domain
:
automated matches
(9)
Human (Homo sapiens) [TaxId: 9606]
(9)
2a
d3h7wa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3h7wA00 (A:236-349)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta-Lactamase
(202)
Homologous Superfamily
:
[code=3.30.450.20, no name defined]
(117)
Human (Homo sapiens)
(9)
1a
3h7wA00
A:236-349
[
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
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 (48 KB)
Header - Asym.Unit
Biol.Unit 1 (43 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
3H7W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help