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3K72
Biol. Unit 1
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (534 KB)
Biol.Unit 2 (536 KB)
Biol.Unit 3, α-C (2.1 MB)
Biol.Unit 3 (2.1 MB)
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(1)
Title
:
STRUCTURE OF INTEGRIN ALPHAX BETA2
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
:
3.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (2x)
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, 16)
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)
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)
2j: ALPHA-D-MANNOSE (MANj)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MAN
5
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:40 , ALA A:41 , ASN A:42 , NAG A:3043
BINDING SITE FOR RESIDUE NAG A 3042
02
AC2
SOFTWARE
NAG A:3042
BINDING SITE FOR RESIDUE NAG A 3043
03
AC3
SOFTWARE
PHE A:354 , ASN A:373 , SER A:375 , GLN A:376 , NAG A:3374
BINDING SITE FOR RESIDUE NAG A 3373
04
AC4
SOFTWARE
GLN A:376 , NAG A:3373 , MAN A:3375
BINDING SITE FOR RESIDUE NAG A 3374
05
AC5
SOFTWARE
NAG A:3374 , MAN A:3376 , MAN A:3377
BINDING SITE FOR RESIDUE MAN A 3375
06
AC6
SOFTWARE
MAN A:3375
BINDING SITE FOR RESIDUE MAN A 3376
07
AC7
SOFTWARE
MAN A:3375
BINDING SITE FOR RESIDUE MAN A 3377
08
AC8
SOFTWARE
THR A:676 , ASN A:678
BINDING SITE FOR RESIDUE NAG A 3678
09
AC9
SOFTWARE
THR A:657 , ASP A:659 , ASN A:716 , TYR A:741 , NAG A:3717
BINDING SITE FOR RESIDUE NAG A 3716
10
BC1
SOFTWARE
NAG A:3716 , MAN A:3718
BINDING SITE FOR RESIDUE NAG A 3717
11
BC2
SOFTWARE
NAG A:3717
BINDING SITE FOR RESIDUE MAN A 3718
12
BC3
SOFTWARE
ASP A:447 , ASP A:449 , ASP A:451 , SER A:453 , ASP A:455
BINDING SITE FOR RESIDUE CA A 2005
13
BC4
SOFTWARE
ASP A:511 , VAL A:512 , ASN A:513 , ASP A:515 , LEU A:517 , ASP A:519
BINDING SITE FOR RESIDUE CA A 2006
14
BC5
SOFTWARE
ASP A:574 , THR A:576 , ASP A:578 , LEU A:580 , ASP A:582
BINDING SITE FOR RESIDUE CA A 2007
15
BC6
SOFTWARE
ASN A:880 , SER A:882 , NAG A:3881
BINDING SITE FOR RESIDUE NAG A 3880
16
BC7
SOFTWARE
VAL A:834 , NAG A:3880 , MAN A:3882
BINDING SITE FOR RESIDUE NAG A 3881
17
BC8
SOFTWARE
NAG A:3881
BINDING SITE FOR RESIDUE MAN A 3882
18
BC9
SOFTWARE
ALA B:92 , ASN B:94
BINDING SITE FOR RESIDUE NAG B 3094
19
CC1
SOFTWARE
SER B:116 , ASP B:119 , ASP B:120 , GLU B:325
BINDING SITE FOR RESIDUE CA B 2002
20
CC2
SOFTWARE
ASN B:479
BINDING SITE FOR RESIDUE NAG B 3479
[
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 A, )
02: VAR_003984 (D106N, chain B, )
03: VAR_065661 (D106Y, chain B, )
04: VAR_013402 (S116P, chain B, )
05: VAR_003985 (L127P, chain B, )
06: VAR_003986 (G147R, chain B, )
07: VAR_003987 (P156L, chain B, )
08: VAR_003988 (K174T, chain B, )
09: VAR_065662 (A217T, chain B, )
10: VAR_013403 (G251R, chain B, )
11: VAR_003989 (G262S, chain B, )
12: VAR_065663 (D278V, chain B, )
13: VAR_003990 (N329S, chain B, )
14: VAR_030035 (Q332H, chain B, )
15: VAR_031926 (P498R, chain A, )
16: VAR_031927 (E528K, chain A, )
17: VAR_059363 (I545V, chain A, )
18: VAR_003991 (R564W, chain B, )
19: VAR_003992 (R571C, chain B, )
20: VAR_031928 (F952L, chain A, )
21: VAR_066662 (A993V, chain A, )
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
A
W
29
R
02
UniProt
VAR_003984
D
128
N
ITB2_HUMAN
Disease (LAD1)
137852615
B
D
106
N
03
UniProt
VAR_065661
D
128
Y
ITB2_HUMAN
Disease (LAD1)
137852615
B
D
106
Y
04
UniProt
VAR_013402
S
138
P
ITB2_HUMAN
Disease (LAD1)
137852617
B
S
116
P
05
UniProt
VAR_003985
L
149
P
ITB2_HUMAN
Disease (LAD1)
137852611
B
L
127
P
06
UniProt
VAR_003986
G
169
R
ITB2_HUMAN
Disease (LAD1)
137852612
B
G
147
R
07
UniProt
VAR_003987
P
178
L
ITB2_HUMAN
Disease (LAD1)
137852614
B
P
156
L
08
UniProt
VAR_003988
K
196
T
ITB2_HUMAN
Disease (LAD1)
137852610
B
K
174
T
09
UniProt
VAR_065662
A
239
T
ITB2_HUMAN
Disease (LAD1)
179363873
B
A
217
T
10
UniProt
VAR_013403
G
273
R
ITB2_HUMAN
Disease (LAD1)
137852618
B
G
251
R
11
UniProt
VAR_003989
G
284
S
ITB2_HUMAN
Disease (LAD1)
137852616
B
G
262
S
12
UniProt
VAR_065663
D
300
V
ITB2_HUMAN
Disease (LAD1)
179363874
B
D
278
V
13
UniProt
VAR_003990
N
351
S
ITB2_HUMAN
Disease (LAD1)
137852613
B
N
329
S
14
UniProt
VAR_030035
Q
354
H
ITB2_HUMAN
Polymorphism
235330
B
Q
332
H
15
UniProt
VAR_031926
P
517
R
ITAX_HUMAN
Polymorphism
2230429
A
P
498
R
16
UniProt
VAR_031927
E
547
K
ITAX_HUMAN
Polymorphism
17853815
A
E
528
K
17
UniProt
VAR_059363
I
564
V
ITAX_HUMAN
Polymorphism
2230430
A
I
545
V
18
UniProt
VAR_003991
R
586
W
ITB2_HUMAN
Disease (LAD1)
5030672
B
R
564
W
19
UniProt
VAR_003992
R
593
C
ITB2_HUMAN
Disease (LAD1)
137852609
B
R
571
C
20
UniProt
VAR_031928
F
971
L
ITAX_HUMAN
Polymorphism
2230427
A
F
952
L
21
UniProt
VAR_066662
A
1012
V
ITAX_HUMAN
Polymorphism
181404376
A
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 (A:4-59,A:60-119,A:326-372,A:425-48...)
2: EGF_1 (B:448-459)
3: EGF_2 (B:448-461)
4: INTEGRIN_BETA (B:484-497)
;
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
A:4-59
-
A:60-119
-
A:326-372
-
A:425-485
-
A:373-424
-
A:488-546
-
A:551-611
-
2
EGF_1
PS00022
EGF-like domain signature 1.
ITB2_HUMAN
470-481
562-573
2
B:448-459
-
B:540-551
-
3
EGF_2
PS01186
EGF-like domain signature 2.
ITB2_HUMAN
470-483
562-575
601-615
3
B:448-461
-
B:540-553
-
B:579-593
-
4
INTEGRIN_BETA
PS00243
Integrins beta chain cysteine-rich domain signature.
ITB2_HUMAN
506-519
549-564
590-603
3
B:484-497
-
B:527-542
-
B:568-581
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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:
Select:
Label:
Sorry, no Info available
[
close CATH info
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Pfam Domains
(4, 8)
Info
all PFAM domains
1a: PFAM_FG_GAP_3k72C01 (C:502-537)
1b: PFAM_FG_GAP_3k72C02 (C:502-537)
2a: PFAM_Integrin_alpha2_3k72C03 (C:596-1013)
2b: PFAM_Integrin_alpha2_3k72C04 (C:596-1013)
3a: PFAM_Integrin_B_tail_3k72D01 (D:600-673)
3b: PFAM_Integrin_B_tail_3k72D02 (D:600-673)
4a: PFAM_Integrin_beta_3k72D03 (D:10-425)
4b: PFAM_Integrin_beta_3k72D04 (D:10-425)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
FG-GAP
(14)
Homo sapiens (Human)
(14)
1a
FG-GAP-3k72C01
C:502-537
1b
FG-GAP-3k72C02
C:502-537
Clan
:
E-set
(290)
Family
:
Integrin_alpha2
(14)
Homo sapiens (Human)
(14)
2a
Integrin_alpha2-3k72C03
C:596-1013
2b
Integrin_alpha2-3k72C04
C:596-1013
Clan
:
no clan defined [family: Integrin_B_tail]
(8)
Family
:
Integrin_B_tail
(8)
Homo sapiens (Human)
(8)
3a
Integrin_B_tail-3k72D01
D:600-673
3b
Integrin_B_tail-3k72D02
D:600-673
Clan
:
no clan defined [family: Integrin_beta]
(18)
Family
:
Integrin_beta
(18)
Homo sapiens (Human)
(18)
4a
Integrin_beta-3k72D03
D:10-425
4b
Integrin_beta-3k72D04
D:10-425
[
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]
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Asym.Unit (1.0 MB)
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