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3K6S
Biol. Unit 2
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Asym.Unit (2.1 MB)
Biol.Unit 1 (584 KB)
Biol.Unit 2 (538 KB)
Biol.Unit 3 (532 KB)
Biol.Unit 4 (529 KB)
Biol.Unit 5, α-C (2.1 MB)
Biol.Unit 5 (2.1 MB)
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(1)
Title
:
STRUCTURE OF INTEGRIN ALPHAXBETA2 ECTODOMAIN
Authors
:
C. Xie, J. Zhu, X. Chen, L. Mi, N. Nishida, T. A. Springer
Date
:
09 Oct 09 (Deposition) - 12 Jan 10 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
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 Receptor, Adhesion Molecule, Cell Adhesion, 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
(1, 9)
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)
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)
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
-1
Ligand/Ion
ALPHA-D-MANNOSE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: CC1 (SOFTWARE)
02: CC2 (SOFTWARE)
03: CC3 (SOFTWARE)
04: CC4 (SOFTWARE)
05: CC5 (SOFTWARE)
06: CC6 (SOFTWARE)
07: CC7 (SOFTWARE)
08: CC8 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: DC3 (SOFTWARE)
13: DC4 (SOFTWARE)
14: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC1
SOFTWARE
ALA C:40 , ALA C:41 , ASN C:42 , NAG C:3043
BINDING SITE FOR RESIDUE NAG C 3042
02
CC2
SOFTWARE
NAG C:3042
BINDING SITE FOR RESIDUE NAG C 3043
03
CC3
SOFTWARE
PHE C:354 , ASN C:373 , GLN C:376 , NAG C:3374
BINDING SITE FOR RESIDUE NAG C 3373
04
CC4
SOFTWARE
GLN C:376 , NAG C:3373
BINDING SITE FOR RESIDUE NAG C 3374
05
CC5
SOFTWARE
THR C:676 , ASN C:678
BINDING SITE FOR RESIDUE NAG C 3678
06
CC6
SOFTWARE
THR C:657 , ASP C:659 , ASN C:716 , THR C:718 , TYR C:741 , NAG C:3717
BINDING SITE FOR RESIDUE NAG C 3716
07
CC7
SOFTWARE
NAG C:3716
BINDING SITE FOR RESIDUE NAG C 3717
08
CC8
SOFTWARE
THR C:801 , VAL C:834 , ASN C:880
BINDING SITE FOR RESIDUE NAG C 3880
09
CC9
SOFTWARE
ASP C:447 , ASP C:449 , ASP C:451 , SER C:453 , ASP C:455
BINDING SITE FOR RESIDUE CA C 2005
10
DC1
SOFTWARE
ASP C:511 , VAL C:512 , ASN C:513 , GLY C:514 , ASP C:515 , LEU C:517 , ASP C:519
BINDING SITE FOR RESIDUE CA C 2006
11
DC2
SOFTWARE
ASP C:574 , THR C:576 , ASP C:578 , LEU C:580 , ASP C:582
BINDING SITE FOR RESIDUE CA C 2007
12
DC3
SOFTWARE
ASN D:94
BINDING SITE FOR RESIDUE NAG D 3094
13
DC4
SOFTWARE
SER D:116 , ASP D:119 , ASP D:120 , GLU D:325
BINDING SITE FOR RESIDUE CA D 2002
14
EC1
SOFTWARE
ARG D:426 , THR E:676 , ASN E:678
BINDING SITE FOR RESIDUE NAG E 3678
[
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 C, )
02: VAR_003984 (D106N, chain D, )
03: VAR_065661 (D106Y, chain D, )
04: VAR_013402 (S116P, chain D, )
05: VAR_003985 (L127P, chain D, )
06: VAR_003986 (G147R, chain D, )
07: VAR_003987 (P156L, chain D, )
08: VAR_003988 (K174T, chain D, )
09: VAR_065662 (A217T, chain D, )
10: VAR_013403 (G251R, chain D, )
11: VAR_003989 (G262S, chain D, )
12: VAR_065663 (D278V, chain D, )
13: VAR_003990 (N329S, chain D, )
14: VAR_030035 (Q332H, chain D, )
15: VAR_031926 (P498R, chain C, )
16: VAR_031927 (E528K, chain C, )
17: VAR_059363 (I545V, chain C, )
18: VAR_003991 (R564W, chain D, )
19: VAR_003992 (R571C, chain D, )
20: VAR_031928 (F952L, chain C, )
21: VAR_066662 (A993V, chain C, )
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
C
W
29
R
02
UniProt
VAR_003984
D
128
N
ITB2_HUMAN
Disease (LAD1)
137852615
D
D
106
N
03
UniProt
VAR_065661
D
128
Y
ITB2_HUMAN
Disease (LAD1)
137852615
D
D
106
Y
04
UniProt
VAR_013402
S
138
P
ITB2_HUMAN
Disease (LAD1)
137852617
D
S
116
P
05
UniProt
VAR_003985
L
149
P
ITB2_HUMAN
Disease (LAD1)
137852611
D
L
127
P
06
UniProt
VAR_003986
G
169
R
ITB2_HUMAN
Disease (LAD1)
137852612
D
G
147
R
07
UniProt
VAR_003987
P
178
L
ITB2_HUMAN
Disease (LAD1)
137852614
D
P
156
L
08
UniProt
VAR_003988
K
196
T
ITB2_HUMAN
Disease (LAD1)
137852610
D
K
174
T
10
UniProt
VAR_065662
A
239
T
ITB2_HUMAN
Disease (LAD1)
179363873
D
A
217
T
12
UniProt
VAR_013403
G
273
R
ITB2_HUMAN
Disease (LAD1)
137852618
D
G
251
R
13
UniProt
VAR_003989
G
284
S
ITB2_HUMAN
Disease (LAD1)
137852616
D
G
262
S
14
UniProt
VAR_065663
D
300
V
ITB2_HUMAN
Disease (LAD1)
179363874
D
D
278
V
15
UniProt
VAR_003990
N
351
S
ITB2_HUMAN
Disease (LAD1)
137852613
D
N
329
S
16
UniProt
VAR_030035
Q
354
H
ITB2_HUMAN
Polymorphism
235330
D
Q
332
H
17
UniProt
VAR_031926
P
517
R
ITAX_HUMAN
Polymorphism
2230429
C
P
498
R
18
UniProt
VAR_031927
E
547
K
ITAX_HUMAN
Polymorphism
17853815
C
E
528
K
19
UniProt
VAR_059363
I
564
V
ITAX_HUMAN
Polymorphism
2230430
C
I
545
V
20
UniProt
VAR_003991
R
586
W
ITB2_HUMAN
Disease (LAD1)
5030672
D
R
564
W
21
UniProt
VAR_003992
R
593
C
ITB2_HUMAN
Disease (LAD1)
137852609
D
R
571
C
22
UniProt
VAR_031928
F
971
L
ITAX_HUMAN
Polymorphism
2230427
C
F
952
L
23
UniProt
VAR_066662
A
1012
V
ITAX_HUMAN
Polymorphism
181404376
C
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 (C:4-59,C:60-119,C:326-372,C:425-48...)
3: EGF_1 (D:448-459,D:540-551)
4: EGF_2 (D:448-461,D:540-553,D:579-593)
5: INTEGRIN_BETA (D:484-497,D:527-542,D: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
-
C:4-59
-
-
-
C:60-119
-
-
-
C:326-372
-
-
-
C:425-485
-
-
-
C:373-424
-
-
-
C:488-546
-
-
-
C: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
-
D:448-459
-
-
-
D:540-551
-
-
4
EGF_2
PS01186
EGF-like domain signature 2.
ITB2_HUMAN
470-483
562-575
601-615
3
-
D:448-461
-
-
-
D:540-553
-
-
-
D:579-593
-
-
5
INTEGRIN_BETA
PS00243
Integrins beta chain cysteine-rich domain signature.
ITB2_HUMAN
506-519
549-564
590-603
3
-
D:484-497
-
-
-
D:527-542
-
-
-
D: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:
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Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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 C
Chain D
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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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)
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show SS bonds with a radius of 100 units (=0.4Å)
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