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.
3NRU
Asym. Unit
Info
Asym.Unit (682 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 10 (63 KB)
Biol.Unit 11 (59 KB)
Biol.Unit 12 (58 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (63 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (63 KB)
Biol.Unit 6 (62 KB)
Biol.Unit 7 (63 KB)
Biol.Unit 8 (60 KB)
Biol.Unit 9 (61 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LIGAND BINDING DOMAIN OF EPHA7
Authors
:
J. R. Walker, L. Yermekbayeva, A. Seitova, J. Kania, C. Bountra, J. Weig C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Date
:
30 Jun 10 (Deposition) - 08 Dec 10 (Release) - 08 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: K (1x)
Biol. Unit 12: L (1x)
Keywords
:
Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Walker, L. Yermekbayeva, A. Seitova, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Ephrin A7 Ligand Binding Domain
To Be Published
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
SO4
10
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:139 , HOH A:341 , ASN C:137 , ARG G:139
BINDING SITE FOR RESIDUE SO4 G 301
02
AC2
SOFTWARE
THR B:130
BINDING SITE FOR RESIDUE CL B 300
03
AC3
SOFTWARE
ASN B:137 , ARG B:139 , ARG E:139 , ASN E:141
BINDING SITE FOR RESIDUE SO4 B 301
04
AC4
SOFTWARE
ARG B:139 , GLU B:140 , ASN B:141 , LYS D:179
BINDING SITE FOR RESIDUE SO4 B 302
05
AC5
SOFTWARE
THR A:156 , LYS B:39 , LYS B:199 , HOH B:384 , ARG G:107
BINDING SITE FOR RESIDUE SO4 B 303
06
AC6
SOFTWARE
THR C:130
BINDING SITE FOR RESIDUE CL C 300
07
AC7
SOFTWARE
ARG A:139 , ASN A:141 , HOH A:313 , HOH A:360 , ASN C:137 , ARG C:139
BINDING SITE FOR RESIDUE SO4 A 301
08
AC8
SOFTWARE
ARG D:139 , GLU D:140 , ASN D:141 , HOH D:337 , ASN E:137 , ARG E:139 , LEU E:142 , HOH E:342
BINDING SITE FOR RESIDUE SO4 D 301
09
AC9
SOFTWARE
ASN B:137 , ARG D:139 , ARG E:139
BINDING SITE FOR RESIDUE SO4 D 302
10
BC1
SOFTWARE
ASN A:137 , ARG A:139 , HOH A:364 , ARG G:139 , GLU G:140 , ASN G:141
BINDING SITE FOR RESIDUE SO4 G 217
11
BC2
SOFTWARE
ARG C:139 , GLU C:140 , ASN C:141 , LYS G:179
BINDING SITE FOR RESIDUE SO4 C 302
12
BC3
SOFTWARE
ARG J:107 , LYS K:39 , LYS K:199 , THR L:156
BINDING SITE FOR RESIDUE SO4 J 301
[
close Site info
]
SAPs(SNPs)/Variants
(2, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_022105 (I138V, chain A/B/C/D/E/F/G/H/I/J/K/L, )
2: VAR_042150 (E170K, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_022105
I
138
V
EPHA7_HUMAN
Polymorphism
2278107
A/B/C/D/E/F/G/H/I/J/K/L
I
138
V
2
UniProt
VAR_042150
E
170
K
EPHA7_HUMAN
Unclassified
---
A/B/C/D/E/F/G/H/I/J/K/L
E
170
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: EPH_LBD (A:32-204,B:32-204,C:32-204,D:32-20...)
2: RECEPTOR_TYR_KIN_V_1 (A:186-204,B:186-204,C:186-204,D:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EPH_LBD
PS51550
Eph receptor ligand-binding domain profile.
EPHA7_HUMAN
32-210
12
A:32-204
B:32-204
C:32-204
D:32-204
E:32-204
F:32-204
G:32-204
H:32-204
I:32-204
J:32-204
K:32-204
L:32-202
2
RECEPTOR_TYR_KIN_V_1
PS00790
Receptor tyrosine kinase class V signature 1.
EPHA7_HUMAN
186-206
12
A:186-204
B:186-204
C:186-204
D:186-204
E:186-204
F:186-204
G:186-204
H:186-204
I:186-204
J:186-204
K:186-204
L:186-202
[
close PROSITE info
]
Exons
(3, 36)
Info
All Exons
Exon 1.1c (A:32-33 | B:32-33 | C:31-33 | D:31...)
Exon 1.2 (A:33-54 (gaps) | B:33-54 (gaps) | ...)
Exon 1.3a (A:55-204 (gaps) | B:55-204 (gaps) ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1c
2: Boundary 1.1c/1.2
3: Boundary 1.2/1.3a
4: Boundary 1.3a/1.4
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
1.1c
ENST00000369303
1c
ENSE00001941413
chr6:
94129244-94128963
282
EPHA7_HUMAN
1-33
33
12
A:32-33
B:32-33
C:31-33
D:31-33
E:31-33
F:31-33
G:30-33
H:31-33
I:31-33
J:31-33
K:31-33
L:32-33
2
2
3
3
3
3
4
3
3
3
3
2
1.2
ENST00000369303
2
ENSE00000974737
chr6:
94124485-94124421
65
EPHA7_HUMAN
33-54
22
12
A:33-54 (gaps)
B:33-54 (gaps)
C:33-54 (gaps)
D:33-54
E:33-54 (gaps)
F:33-54 (gaps)
G:33-54
H:33-54 (gaps)
I:33-54 (gaps)
J:33-54
K:33-54 (gaps)
L:33-54 (gaps)
22
22
22
22
22
22
22
22
22
22
22
22
1.3a
ENST00000369303
3a
ENSE00000918734
chr6:
94120888-94120219
670
EPHA7_HUMAN
55-278
224
12
A:55-204 (gaps)
B:55-204 (gaps)
C:55-204 (gaps)
D:55-204 (gaps)
E:55-204 (gaps)
F:55-204 (gaps)
G:55-204 (gaps)
H:55-204 (gaps)
I:55-204 (gaps)
J:55-204 (gaps)
K:55-204 (gaps)
L:55-202 (gaps)
150
150
150
150
150
150
150
150
150
150
150
148
1.4
ENST00000369303
4
ENSE00000974738
chr6:
94068129-94067974
156
EPHA7_HUMAN
278-330
53
0
-
-
1.5
ENST00000369303
5
ENSE00000974739
chr6:
94066770-94066435
336
EPHA7_HUMAN
330-442
113
0
-
-
1.6
ENST00000369303
6
ENSE00001309196
chr6:
93982140-93982016
125
EPHA7_HUMAN
442-483
42
0
-
-
1.7b
ENST00000369303
7b
ENSE00000974741
chr6:
93979378-93979195
184
EPHA7_HUMAN
484-545
62
0
-
-
1.8
ENST00000369303
8
ENSE00001084117
chr6:
93974420-93974312
109
EPHA7_HUMAN
545-581
37
0
-
-
1.9
ENST00000369303
9
ENSE00000974743
chr6:
93973633-93973578
56
EPHA7_HUMAN
581-600
20
0
-
-
1.10
ENST00000369303
10
ENSE00000974744
chr6:
93969197-93969072
126
EPHA7_HUMAN
600-642
43
0
-
-
1.11
ENST00000369303
11
ENSE00000974745
chr6:
93968002-93967817
186
EPHA7_HUMAN
642-704
63
0
-
-
1.12
ENST00000369303
12
ENSE00000974746
chr6:
93967241-93967180
62
EPHA7_HUMAN
704-724
21
0
-
-
1.13
ENST00000369303
13
ENSE00002150360
chr6:
93965755-93965546
210
EPHA7_HUMAN
725-794
70
0
-
-
1.14
ENST00000369303
14
ENSE00002154876
chr6:
93964514-93964365
150
EPHA7_HUMAN
795-844
50
0
-
-
1.15
ENST00000369303
15
ENSE00000974749
chr6:
93956703-93956510
194
EPHA7_HUMAN
845-909
65
0
-
-
1.16
ENST00000369303
16
ENSE00000974750
chr6:
93955171-93955016
156
EPHA7_HUMAN
909-961
53
0
-
-
1.17
ENST00000369303
17
ENSE00001449448
chr6:
93953258-93949738
3521
EPHA7_HUMAN
961-998
38
0
-
-
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3nrua_ (A:)
1b: SCOP_d3nrud_ (D:)
1c: SCOP_d3nrue_ (E:)
1d: SCOP_d3nruf_ (F:)
1e: SCOP_d3nrug_ (G:)
1f: SCOP_d3nruh_ (H:)
1g: SCOP_d3nrui_ (I:)
1h: SCOP_d3nruj_ (J:)
1i: SCOP_d3nruk_ (K:)
1j: SCOP_d3nrul_ (L:)
1k: SCOP_d3nrub_ (B:)
1l: SCOP_d3nruc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
Ephrin receptor ligand binding domain
(15)
Protein domain
:
automated matches
(9)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d3nrua_
A:
1b
d3nrud_
D:
1c
d3nrue_
E:
1d
d3nruf_
F:
1e
d3nrug_
G:
1f
d3nruh_
H:
1g
d3nrui_
I:
1h
d3nruj_
J:
1i
d3nruk_
K:
1j
d3nrul_
L:
1k
d3nrub_
B:
1l
d3nruc_
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
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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 (682 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 10 (63 KB)
Header - Biol.Unit 10
Biol.Unit 11 (59 KB)
Header - Biol.Unit 11
Biol.Unit 12 (58 KB)
Header - Biol.Unit 12
Biol.Unit 2 (63 KB)
Header - Biol.Unit 2
Biol.Unit 3 (63 KB)
Header - Biol.Unit 3
Biol.Unit 4 (62 KB)
Header - Biol.Unit 4
Biol.Unit 5 (63 KB)
Header - Biol.Unit 5
Biol.Unit 6 (62 KB)
Header - Biol.Unit 6
Biol.Unit 7 (63 KB)
Header - Biol.Unit 7
Biol.Unit 8 (60 KB)
Header - Biol.Unit 8
Biol.Unit 9 (61 KB)
Header - Biol.Unit 9
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
3NRU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help