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3WN5
Asym. Unit
Info
Asym.Unit (214 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ASYMMETRICALLY ENGINEERED FC VARIANT IN COMPLEX WITH FCGRIIIA
Authors
:
S. Kadono, F. Mimoto, H. Katada, T. Igawa, T. Kamikawa, K. Hattori
Date
:
05 Dec 13 (Deposition) - 19 Nov 14 (Release) - 19 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.78
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Receptor Complex, Fc Receptor, Antibody, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Mimoto, S. Kadono, H. Katada, T. Igawa, T. Kamikawa, K. Hattori
Crystal Structure Of A Novel Asymmetrically Engineered Fc Variant With Improved Affinity For Fc Gamma Rs.
Mol. Immunol. V. 58 132 2014
[
close entry info
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Hetero Components
(6, 61)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
2a: BETA-L-FUCOSE (FULa)
2b: BETA-L-FUCOSE (FULb)
2c: BETA-L-FUCOSE (FULc)
2d: BETA-L-FUCOSE (FULd)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
4a: IODIDE ION (IODa)
4b: IODIDE ION (IODb)
4c: IODIDE ION (IODc)
4d: IODIDE ION (IODd)
4e: IODIDE ION (IODe)
4f: IODIDE ION (IODf)
4g: IODIDE ION (IODg)
4h: IODIDE ION (IODh)
4i: IODIDE ION (IODi)
4j: IODIDE ION (IODj)
4k: IODIDE ION (IODk)
4l: IODIDE ION (IODl)
4m: IODIDE ION (IODm)
4n: IODIDE ION (IODn)
4o: IODIDE ION (IODo)
4p: IODIDE ION (IODp)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
5e: ALPHA-D-MANNOSE (MANe)
5f: ALPHA-D-MANNOSE (MANf)
5g: ALPHA-D-MANNOSE (MANg)
5h: ALPHA-D-MANNOSE (MANh)
5i: ALPHA-D-MANNOSE (MANi)
5j: ALPHA-D-MANNOSE (MANj)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6m: N-ACETYL-D-GLUCOSAMINE (NAGm)
6n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6o: N-ACETYL-D-GLUCOSAMINE (NAGo)
6p: N-ACETYL-D-GLUCOSAMINE (NAGp)
6q: N-ACETYL-D-GLUCOSAMINE (NAGq)
6r: N-ACETYL-D-GLUCOSAMINE (NAGr)
6s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6t: N-ACETYL-D-GLUCOSAMINE (NAGt)
6u: N-ACETYL-D-GLUCOSAMINE (NAGu)
6v: N-ACETYL-D-GLUCOSAMINE (NAGv)
6w: N-ACETYL-D-GLUCOSAMINE (NAGw)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
5
Ligand/Ion
BETA-D-MANNOSE
2
FUL
4
Ligand/Ion
BETA-L-FUCOSE
3
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
4
IOD
16
Ligand/Ion
IODIDE ION
5
MAN
10
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
23
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG A:1005
BINDING SITE FOR RESIDUE IOD A 1011
02
AC2
SOFTWARE
SER A:354 , THR B:350
BINDING SITE FOR RESIDUE IOD B 1010
03
AC3
SOFTWARE
VAL B:240
BINDING SITE FOR RESIDUE IOD B 1011
04
AC4
SOFTWARE
NAG B:1005
BINDING SITE FOR RESIDUE IOD B 1012
05
AC5
SOFTWARE
ARG C:15 , ALA C:92
BINDING SITE FOR RESIDUE IOD C 208
06
AC6
SOFTWARE
GLU C:43
BINDING SITE FOR RESIDUE IOD C 209
07
AC7
SOFTWARE
LYS D:414
BINDING SITE FOR RESIDUE IOD D 1009
08
AC8
SOFTWARE
CYS D:356 , THR E:350
BINDING SITE FOR RESIDUE IOD E 1010
09
AC9
SOFTWARE
SER E:254
BINDING SITE FOR RESIDUE IOD E 1011
10
BC1
SOFTWARE
VAL E:240 , LYS E:334
BINDING SITE FOR RESIDUE IOD E 1012
11
BC2
SOFTWARE
GLU F:43 , GLU F:65
BINDING SITE FOR RESIDUE IOD F 205
12
BC3
SOFTWARE
TYR F:30
BINDING SITE FOR RESIDUE IOD F 206
13
BC4
SOFTWARE
TRP F:87
BINDING SITE FOR RESIDUE IOD F 207
14
BC5
SOFTWARE
PHE A:241 , PHE A:243 , PRO A:245 , LYS A:246 , ASP A:249 , GLU A:258 , THR A:260 , VAL A:262 , VAL A:264 , ASP A:265 , GLN A:295 , ASN A:297 , THR A:299 , ARG A:301 , GLU A:334 , IOD A:1011
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 297 RESIDUES 1001 TO 1009
15
BC6
SOFTWARE
MET B:239 , PHE B:241 , PHE B:243 , PRO B:244 , LYS B:246 , GLU B:258 , THR B:260 , VAL B:264 , ASP B:265 , GLN B:295 , TYR B:296 , ASN B:297 , ARG B:301 , LYS B:334 , IOD B:1012 , TYR C:129 , NAG C:201 , NAG C:202 , BMA C:203 , MAN C:204
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 297 RESIDUES 1001 TO 1009
16
BC7
SOFTWARE
HIS C:41 , ASN C:42 , ASP C:61 , SER C:63
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 42 RESIDUES 206 TO 207
17
BC8
SOFTWARE
NAG B:1001 , FUL B:1007 , ARG C:152 , ASN C:159
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 159 RESIDUES 201 TO 205
18
BC9
SOFTWARE
PHE D:241 , PHE D:243 , LYS D:246 , VAL D:264 , ASP D:265 , GLN D:295 , ASN D:297 , THR D:299 , ARG D:301 , GLU D:334 , HOH D:1102 , HOH D:1103
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 297 RESIDUES 1001 TO 1008
19
CC1
SOFTWARE
MET E:239 , PHE E:241 , PHE E:243 , PRO E:244 , LYS E:246 , GLU E:258 , THR E:260 , VAL E:264 , ASP E:265 , ASN E:297 , THR E:299 , ARG E:301 , LYS E:334 , HOH E:1102
BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 297 RESIDUES 1001 TO 1009
20
CC2
SOFTWARE
HIS F:41 , ASN F:42 , ASP F:61 , SER F:63
BINDING SITE FOR CHAIN F OF SUGAR BOUND TO ASN F 42 RESIDUES 202 TO 203
21
CC3
SOFTWARE
ASN F:159 , VAL F:160 , SER F:161
BINDING SITE FOR MONO-SACCHARIDE NAG F 201 BOUND TO ASN F 159
[
close Site info
]
SAPs(SNPs)/Variants
(7, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_008800 (L45H, chain C/F, )
2: VAR_008799 (L45R, chain C/F, )
3: VAR_058398 (G126D, chain C/F, )
4: VAR_058399 (Y137H, chain C/F, )
5: VAR_003960 (V155V, chain C/F, )
6: VAR_003887 (C356E, chain A/B/D/E, )
7: VAR_003888 (L358M, chain A/B/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_008800
L
66
H
FCG3A_HUMAN
Disease (IMD20)
10127939
C/F
L
45
H
2
UniProt
VAR_008799
L
66
R
FCG3A_HUMAN
Polymorphism
10127939
C/F
L
45
R
3
UniProt
VAR_058398
G
147
D
FCG3A_HUMAN
Polymorphism
443082
C/F
G
126
D
4
UniProt
VAR_058399
Y
158
H
FCG3A_HUMAN
Polymorphism
396716
C/F
Y
137
H
5
UniProt
VAR_003960
F
176
V
FCG3A_HUMAN
Polymorphism
396991
C/F
V
155
V
6
UniProt
VAR_003887
D
239
E
IGHG1_HUMAN
Unclassified
---
A/B/D/E
C
356
E
7
UniProt
VAR_003888
L
241
M
IGHG1_HUMAN
Unclassified
---
A/B/D/E
L
358
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (-|A:423-429,B:423-429,D:423-429,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGHG1_HUMAN
81-87
306-312
4
-
A:423-429
B:423-429
D:423-429
E:423-429
[
close PROSITE info
]
Exons
(2, 8)
Info
All Exons
Exon 1.3b (A:233-341 | B:235-341 | D:233-341 ...)
Exon 1.4c (A:341-444 | B:341-444 | D:341-444 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3b
2: Boundary 1.3b/1.4c
3: Boundary 1.4c/-
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
1.1
ENST00000390549
1
ENSE00001838294
chr14:
106209408-106209114
295
IGHG1_HUMAN
1-99
99
0
-
-
1.2
ENST00000390549
2
ENSE00001719055
chr14:
106208722-106208678
45
IGHG1_HUMAN
99-114
16
0
-
-
1.3b
ENST00000390549
3b
ENSE00001776617
chr14:
106208559-106208230
330
IGHG1_HUMAN
114-224
111
4
A:233-341
B:235-341
D:233-341
E:235-341
109
107
109
107
1.4c
ENST00000390549
4c
ENSE00001837466
chr14:
106208132-106207675
458
IGHG1_HUMAN
224-330
107
4
A:341-444
B:341-444
D:341-444
E:341-444
104
104
104
104
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
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:
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Label:
Sorry, no Info available
[
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Atom Selection
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)
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Hetero
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Chain D
Chain E
Chain F
Asymmetric Unit 1
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Asym.Unit (214 KB)
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