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.
3K71
Biol. Unit 3
Info
Asym.Unit (2.1 MB)
Biol.Unit 1 (536 KB)
Biol.Unit 2 (536 KB)
Biol.Unit 3 (538 KB)
Biol.Unit 4 (606 KB)
Biol.Unit 5, α-C (2.1 MB)
Biol.Unit 5 (2.1 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF INTEGRIN ALPHAX BETA2 ECTODOMAIN
Authors
:
C. Xie, J. Zhu, X. Chen, L. Mi, N. Nishida, T. A. Springer
Date
:
11 Oct 09 (Deposition) - 12 Jan 10 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.95
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: A,B,C,D,E,F,G,H (1x)
Keywords
:
Integrin, Cell Adhesion, Cell Receptor, Pyrrolidone Carboxylic Acid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Xie, J. Zhu, X. Chen, L. Mi, N. Nishida, T. A. Springer
Structure Of An Integrin With An Alphai Domain, Complement Receptor Type 4.
Embo J. V. 29 666 2010
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
2i: ALPHA-D-MANNOSE (MANi)
3a: MAGNESIUM ION (MGa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
4ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
4ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
4ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
4ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
4af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
4ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
4ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
4ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
4aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
4ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
4al: N-ACETYL-D-GLUCOSAMINE (NAGal)
4am: N-ACETYL-D-GLUCOSAMINE (NAGam)
4an: N-ACETYL-D-GLUCOSAMINE (NAGan)
4ao: N-ACETYL-D-GLUCOSAMINE (NAGao)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
4p: N-ACETYL-D-GLUCOSAMINE (NAGp)
4q: N-ACETYL-D-GLUCOSAMINE (NAGq)
4r: N-ACETYL-D-GLUCOSAMINE (NAGr)
4s: N-ACETYL-D-GLUCOSAMINE (NAGs)
4t: N-ACETYL-D-GLUCOSAMINE (NAGt)
4u: N-ACETYL-D-GLUCOSAMINE (NAGu)
4v: N-ACETYL-D-GLUCOSAMINE (NAGv)
4w: N-ACETYL-D-GLUCOSAMINE (NAGw)
4x: N-ACETYL-D-GLUCOSAMINE (NAGx)
4y: N-ACETYL-D-GLUCOSAMINE (NAGy)
4z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: DC7 (SOFTWARE)
02: DC8 (SOFTWARE)
03: DC9 (SOFTWARE)
04: EC1 (SOFTWARE)
05: EC2 (SOFTWARE)
06: EC3 (SOFTWARE)
07: EC4 (SOFTWARE)
08: EC5 (SOFTWARE)
09: EC6 (SOFTWARE)
10: EC7 (SOFTWARE)
11: EC8 (SOFTWARE)
12: EC9 (SOFTWARE)
13: FC1 (SOFTWARE)
14: FC2 (SOFTWARE)
15: FC3 (SOFTWARE)
16: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
DC7
SOFTWARE
ALA E:40 , ASN E:42 , NAG E:3043
BINDING SITE FOR RESIDUE NAG E 3042
02
DC8
SOFTWARE
NAG E:3042
BINDING SITE FOR RESIDUE NAG E 3043
03
DC9
SOFTWARE
PHE E:354 , PHE E:371 , ASN E:373 , SER E:375 , GLN E:376 , NAG E:3374
BINDING SITE FOR RESIDUE NAG E 3373
04
EC1
SOFTWARE
GLN E:376 , NAG E:3373 , MAN E:3375
BINDING SITE FOR RESIDUE NAG E 3374
05
EC2
SOFTWARE
NAG E:3374
BINDING SITE FOR RESIDUE MAN E 3375
06
EC3
SOFTWARE
THR E:676 , ASN E:678
BINDING SITE FOR RESIDUE NAG E 3678
07
EC4
SOFTWARE
THR E:657 , ASP E:659 , ASN E:716 , THR E:718 , TYR E:741 , NAG E:3717 , ASP F:501
BINDING SITE FOR RESIDUE NAG E 3716
08
EC5
SOFTWARE
NAG E:3716 , MAN E:3718
BINDING SITE FOR RESIDUE NAG E 3717
09
EC6
SOFTWARE
NAG E:3717
BINDING SITE FOR RESIDUE MAN E 3718
10
EC7
SOFTWARE
THR E:801 , ASN E:880 , THR E:887 , LYS E:892
BINDING SITE FOR RESIDUE NAG E 3880
11
EC8
SOFTWARE
ASP E:447 , ASP E:449 , ASP E:451 , SER E:453 , THR E:454 , ASP E:455
BINDING SITE FOR RESIDUE CA E 2005
12
EC9
SOFTWARE
ASP E:511 , VAL E:512 , ASN E:513 , GLY E:514 , ASP E:515 , LEU E:517
BINDING SITE FOR RESIDUE CA E 2006
13
FC1
SOFTWARE
ASP E:574 , LEU E:575 , THR E:576 , ASP E:578 , LEU E:580 , ASP E:582
BINDING SITE FOR RESIDUE CA E 2007
14
FC2
SOFTWARE
ASN F:94
BINDING SITE FOR RESIDUE NAG F 3094
15
FC3
SOFTWARE
ASN F:479
BINDING SITE FOR RESIDUE NAG F 3479
16
FC4
SOFTWARE
SER F:116 , ASP F:119 , ASP F:120 , GLU F:325
BINDING SITE FOR RESIDUE CA F 2002
[
close Site info
]
SAPs(SNPs)/Variants
(21, 21)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_018672 (W29R, chain E, )
02: VAR_003984 (D106N, chain F, )
03: VAR_065661 (D106Y, chain F, )
04: VAR_013402 (S116P, chain F, )
05: VAR_003985 (L127P, chain F, )
06: VAR_003986 (G147R, chain F, )
07: VAR_003987 (P156L, chain F, )
08: VAR_003988 (K174T, chain F, )
09: VAR_065662 (A217T, chain F, )
10: VAR_013403 (G251R, chain F, )
11: VAR_003989 (G262S, chain F, )
12: VAR_065663 (D278V, chain F, )
13: VAR_003990 (N329S, chain F, )
14: VAR_030035 (Q332H, chain F, )
15: VAR_031926 (P498R, chain E, )
16: VAR_031927 (E528K, chain E, )
17: VAR_059363 (I545V, chain E, )
18: VAR_003991 (R564W, chain F, )
19: VAR_003992 (R571C, chain F, )
20: VAR_031928 (F952L, chain E, )
21: VAR_066662 (A993V, chain E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_018672
W
48
R
ITAX_HUMAN
Polymorphism
2230424
E
W
29
R
02
UniProt
VAR_003984
D
128
N
ITB2_HUMAN
Disease (LAD1)
137852615
F
D
106
N
03
UniProt
VAR_065661
D
128
Y
ITB2_HUMAN
Disease (LAD1)
137852615
F
D
106
Y
04
UniProt
VAR_013402
S
138
P
ITB2_HUMAN
Disease (LAD1)
137852617
F
S
116
P
05
UniProt
VAR_003985
L
149
P
ITB2_HUMAN
Disease (LAD1)
137852611
F
L
127
P
06
UniProt
VAR_003986
G
169
R
ITB2_HUMAN
Disease (LAD1)
137852612
F
G
147
R
07
UniProt
VAR_003987
P
178
L
ITB2_HUMAN
Disease (LAD1)
137852614
F
P
156
L
08
UniProt
VAR_003988
K
196
T
ITB2_HUMAN
Disease (LAD1)
137852610
F
K
174
T
10
UniProt
VAR_065662
A
239
T
ITB2_HUMAN
Disease (LAD1)
179363873
F
A
217
T
12
UniProt
VAR_013403
G
273
R
ITB2_HUMAN
Disease (LAD1)
137852618
F
G
251
R
13
UniProt
VAR_003989
G
284
S
ITB2_HUMAN
Disease (LAD1)
137852616
F
G
262
S
14
UniProt
VAR_065663
D
300
V
ITB2_HUMAN
Disease (LAD1)
179363874
F
D
278
V
15
UniProt
VAR_003990
N
351
S
ITB2_HUMAN
Disease (LAD1)
137852613
F
N
329
S
16
UniProt
VAR_030035
Q
354
H
ITB2_HUMAN
Polymorphism
235330
F
Q
332
H
17
UniProt
VAR_031926
P
517
R
ITAX_HUMAN
Polymorphism
2230429
E
P
498
R
18
UniProt
VAR_031927
E
547
K
ITAX_HUMAN
Polymorphism
17853815
E
E
528
K
19
UniProt
VAR_059363
I
564
V
ITAX_HUMAN
Polymorphism
2230430
E
I
545
V
20
UniProt
VAR_003991
R
586
W
ITB2_HUMAN
Disease (LAD1)
5030672
F
R
564
W
21
UniProt
VAR_003992
R
593
C
ITB2_HUMAN
Disease (LAD1)
137852609
F
R
571
C
22
UniProt
VAR_031928
F
971
L
ITAX_HUMAN
Polymorphism
2230427
E
F
952
L
23
UniProt
VAR_066662
A
1012
V
ITAX_HUMAN
Polymorphism
181404376
E
A
993
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 15)
Info
All PROSITE Patterns/Profiles
1: FG_GAP (E:4-59,E:60-119,E:328-372,E:425-48...)
3: EGF_1 (F:448-459,F:540-551)
4: EGF_2 (F:448-461,F:540-553,F:579-593)
5: INTEGRIN_BETA (F:484-497,F:527-542,F:568-581)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FG_GAP
PS51470
FG-GAP repeat profile.
ITAX_HUMAN
23-78
79-138
340-391
444-504
392-443
507-565
570-630
7
-
-
E:4-59
-
-
-
E:60-119
-
-
-
E:328-372
-
-
-
E:425-485
-
-
-
E:373-424
-
-
-
E:488-546
-
-
-
E:551-611
-
2
VWFA
PS50234
VWFA domain profile.
ITAX_HUMAN
151-329
0
-
3
EGF_1
PS00022
EGF-like domain signature 1.
ITB2_HUMAN
470-481
562-573
2
-
-
F:448-459
-
-
-
F:540-551
-
4
EGF_2
PS01186
EGF-like domain signature 2.
ITB2_HUMAN
470-483
562-575
601-615
3
-
-
F:448-461
-
-
-
F:540-553
-
-
-
F:579-593
-
5
INTEGRIN_BETA
PS00243
Integrins beta chain cysteine-rich domain signature.
ITB2_HUMAN
506-519
549-564
590-603
3
-
-
F:484-497
-
-
-
F:527-542
-
-
-
F:568-581
-
[
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
(5, 17)
Info
all PFAM domains
1a: PFAM_FG_GAP_3k71G01 (G:502-537)
1b: PFAM_FG_GAP_3k71G02 (G:502-537)
1c: PFAM_FG_GAP_3k71G03 (G:502-537)
1d: PFAM_FG_GAP_3k71G04 (G:502-537)
2a: PFAM_Integrin_alpha2_3k71G05 (G:596-1013)
2b: PFAM_Integrin_alpha2_3k71G06 (G:596-1013)
2c: PFAM_Integrin_alpha2_3k71G07 (G:596-1013)
2d: PFAM_Integrin_alpha2_3k71G08 (G:596-1013)
3a: PFAM_Integrin_B_tail_3k71H01 (H:600-673)
3b: PFAM_Integrin_B_tail_3k71H02 (H:600-673)
3c: PFAM_Integrin_B_tail_3k71H03 (H:600-673)
3d: PFAM_Integrin_B_tail_3k71H04 (H:600-673)
4a: PFAM_Integrin_beta_3k71H05 (H:10-425)
4b: PFAM_Integrin_beta_3k71H06 (H:10-425)
4c: PFAM_Integrin_beta_3k71H07 (H:10-425)
4d: PFAM_Integrin_beta_3k71H08 (H:10-425)
5a: PFAM_VWA_3k71G09 (G:132-310)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
FG-GAP
(14)
Homo sapiens (Human)
(14)
1a
FG-GAP-3k71G01
G:502-537
1b
FG-GAP-3k71G02
G:502-537
1c
FG-GAP-3k71G03
G:502-537
1d
FG-GAP-3k71G04
G:502-537
Clan
:
E-set
(290)
Family
:
Integrin_alpha2
(14)
Homo sapiens (Human)
(14)
2a
Integrin_alpha2-3k71G05
G:596-1013
2b
Integrin_alpha2-3k71G06
G:596-1013
2c
Integrin_alpha2-3k71G07
G:596-1013
2d
Integrin_alpha2-3k71G08
G:596-1013
Clan
:
no clan defined [family: Integrin_B_tail]
(8)
Family
:
Integrin_B_tail
(8)
Homo sapiens (Human)
(8)
3a
Integrin_B_tail-3k71H01
H:600-673
3b
Integrin_B_tail-3k71H02
H:600-673
3c
Integrin_B_tail-3k71H03
H:600-673
3d
Integrin_B_tail-3k71H04
H:600-673
Clan
:
no clan defined [family: Integrin_beta]
(18)
Family
:
Integrin_beta
(18)
Homo sapiens (Human)
(18)
4a
Integrin_beta-3k71H05
H:10-425
4b
Integrin_beta-3k71H06
H:10-425
4c
Integrin_beta-3k71H07
H:10-425
4d
Integrin_beta-3k71H08
H:10-425
Clan
:
vWA-like
(60)
Family
:
VWA
(50)
Homo sapiens (Human)
(47)
5a
VWA-3k71G09
G:132-310
[
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 E
Chain F
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 (2.1 MB)
Header - Asym.Unit
Biol.Unit 1 (536 KB)
Header - Biol.Unit 1
Biol.Unit 2 (536 KB)
Header - Biol.Unit 2
Biol.Unit 3 (538 KB)
Header - Biol.Unit 3
Biol.Unit 4 (606 KB)
Header - Biol.Unit 4
Biol.Unit 5 (2.1 MB)
Header - Biol.Unit 5
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
3K71
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help