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3Q3G
Biol. Unit 3
Info
Asym.Unit (421 KB)
Biol.Unit 1 (112 KB)
Biol.Unit 2 (111 KB)
Biol.Unit 3 (109 KB)
Biol.Unit 4 (111 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A-DOMAIN IN COMPLEX WITH ANTIBODY
Authors
:
B. Mahalingam, J. P. Xiong, M. A. Arnaout
Date
:
21 Dec 10 (Deposition) - 30 Nov 11 (Release) - 28 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: C,D,G (1x)
Biol. Unit 2: A,B,E (1x)
Biol. Unit 3: F,H,I (1x)
Biol. Unit 4: J,K,L (1x)
Keywords
:
Immune System-Cell Adhesion Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Mahalingam, K. Ajroud, J. L. Alonso, S. Anand, B. D. Adair, A. L. Horenstein, F. Malavasi, J. P. Xiong, M. A. Arnaout
Stable Coordination Of The Inhibitory Ca2+ Ion At The Metal Ion-Dependent Adhesion Site In Integrin Cd11B/Cd18 By An Antibody-Derived Ligand Aspartate: Implications For Integri Regulation And Structure-Based Drug Design.
J. Immunol. V. 187 6393 2011
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
4
GOL
-1
Ligand/Ion
GLYCEROL
5
NA
-1
Ligand/Ion
SODIUM ION
6
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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Sites
(9, 9)
Info
All Sites
1: AC3 (SOFTWARE)
2: BC3 (SOFTWARE)
3: CC6 (SOFTWARE)
4: CC8 (SOFTWARE)
5: DC3 (SOFTWARE)
6: DC4 (SOFTWARE)
7: DC5 (SOFTWARE)
8: DC6 (SOFTWARE)
9: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
HOH F:1008 , ASP H:107 , SER I:142 , SER I:144 , THR I:209 , ASP I:242 , HOH I:1009
BINDING SITE FOR RESIDUE CA I 500
2
BC3
SOFTWARE
HOH F:1008 , ASP I:242
BINDING SITE FOR RESIDUE EDO F 621
3
CC6
SOFTWARE
ASP D:75 , THR D:76 , SER D:77 , GOL D:702 , ASN H:166 , SER H:169 , THR H:203
BINDING SITE FOR RESIDUE EDO D 614
4
CC8
SOFTWARE
ASP D:58 , ALA D:74 , ASP D:75 , EDO D:614 , HOH D:1232 , GLU H:202
BINDING SITE FOR RESIDUE GOL D 702
5
DC3
SOFTWARE
VAL H:132
BINDING SITE FOR RESIDUE NA H 801
6
DC4
SOFTWARE
LYS H:40
BINDING SITE FOR RESIDUE NA H 802
7
DC5
SOFTWARE
PHE H:29 , ILE H:34 , SER H:100 , GLY H:102 , TYR H:104 , ASP H:112 , TYR H:113
BINDING SITE FOR RESIDUE PEG H 1000
8
DC6
SOFTWARE
ALA H:212 , SER H:213 , SER J:128 , GLU J:129
BINDING SITE FOR RESIDUE EDO J 603
9
EC7
SOFTWARE
PRO H:129 , VAL K:132 , LYS K:219
BINDING SITE FOR RESIDUE EDO K 601
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: VWFA (I:134-312)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VWFA
PS50234
VWFA domain profile.
ITAM_HUMAN
150-328
1
-
-
I:134-312
-
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Exons
(0, 0)
Info
All Exons
View:
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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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d3q3ga1 (A:1-113)
1b: SCOP_d3q3gc1 (C:1-113)
1c: SCOP_d3q3gf1 (F:1-113)
1d: SCOP_d3q3gj1 (J:1-113)
2a: SCOP_d3q3ga2 (A:114-220)
2b: SCOP_d3q3gc2 (C:114-220)
2c: SCOP_d3q3gf2 (F:114-220)
2d: SCOP_d3q3gj2 (J:114-220)
3a: SCOP_d3q3ge_ (E:)
3b: SCOP_d3q3gg_ (G:)
3c: SCOP_d3q3gi_ (I:)
3d: SCOP_d3q3gl_ (L:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3q3ga1
A:1-113
1b
d3q3gc1
C:1-113
1c
d3q3gf1
F:1-113
1d
d3q3gj1
J:1-113
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3q3ga2
A:114-220
2b
d3q3gc2
C:114-220
2c
d3q3gf2
F:114-220
2d
d3q3gj2
J:114-220
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
vWA-like
(111)
Superfamily
:
vWA-like
(111)
Family
:
Integrin A (or I) domain
(84)
Protein domain
:
Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
3a
d3q3ge_
E:
3b
d3q3gg_
G:
3c
d3q3gi_
I:
3d
d3q3gl_
L:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
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 F
Chain H
Chain I
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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set fontsize 20
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Show PDB file:
Asym.Unit (421 KB)
Header - Asym.Unit
Biol.Unit 1 (112 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
Biol.Unit 3 (109 KB)
Header - Biol.Unit 3
Biol.Unit 4 (111 KB)
Header - Biol.Unit 4
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