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Getting 'Exon' information from database.
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Asym. Unit
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Asym.Unit (240 KB)
Biol.Unit 1 (230 KB)
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(1)
Title
:
THE HIGH RESOLUTION CRYSTAL STRUCTURE OF IGE FC
Authors
:
B. Dhaliwal, B. J. Sutton, A. J. Beavil
Date
:
26 Aug 09 (Deposition) - 03 Nov 10 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Immune System, Immunoglobulin Domain, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. D. Holdom, A. M. Davies, J. E. Nettleship, S. C. Bagby, B. Dhaliwal, E. Girardi, J. Hunt, H. J. Gould, A. J. Beavil, J. M. Mcdonnell, R. J. Owens, B. J. Sutton
Conformational Changes In Ige Contribute To Its Uniquely Slow Dissociation Rate From Receptor Fceri
Nat. Struct. Mol. Biol. V. 18 571 2011
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(7, 18)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: TETRAETHYLENE GLYCOL (PG4a)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
7a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
6
SO4
4
Ligand/Ion
SULFATE ION
7
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:362 , GLN A:392 , ASN A:394 , THR A:396 , NAG A:602
BINDING SITE FOR RESIDUE NAG A 946
02
AC2
SOFTWARE
TYR A:339 , LEU A:359 , NAG A:601 , BMA A:603
BINDING SITE FOR RESIDUE NAG A 947
03
AC3
SOFTWARE
TYR A:339 , NAG A:602 , MAN A:604 , MAN A:605 , HOH A:888
BINDING SITE FOR RESIDUE BMA A 948
04
AC4
SOFTWARE
BMA A:603 , HOH A:818
BINDING SITE FOR RESIDUE MAN A 949
05
AC5
SOFTWARE
GLN A:494 , BMA A:603 , HOH A:858
BINDING SITE FOR RESIDUE MAN A 950
06
AC6
SOFTWARE
THR A:493 , GLN A:494 , ARG A:496 , HOH A:754 , HOH A:786 , ARG B:496
BINDING SITE FOR RESIDUE SO4 A 951
07
AC7
SOFTWARE
THR A:407 , ARG A:408
BINDING SITE FOR RESIDUE SO4 A 952
08
AC8
SOFTWARE
ARG A:496 , LYS A:497 , ARG B:308
BINDING SITE FOR RESIDUE SO4 A 953
09
AC9
SOFTWARE
ARG A:419 , ALA A:442 , GLY B:244 , HIS B:246
BINDING SITE FOR RESIDUE GOL A 954
10
BC1
SOFTWARE
ASP A:242 , GLY A:243 , SER B:324 , ARG B:393
BINDING SITE FOR RESIDUE GOL A 955
11
BC2
SOFTWARE
SER A:344 , ILE A:474 , SER A:475 , VAL A:476 , HOH A:817 , HOH A:749
BINDING SITE FOR RESIDUE TRS A 956
12
BC3
SOFTWARE
LYS A:235 , LEU A:253A , LEU A:255 , GLN A:294 , GLU A:296 , HOH A:746 , HOH B:719 , HOH B:701 , LYS B:235 , LEU B:253A , LEU B:255 , GLN B:294 , GLU B:296 , HOH B:919
BINDING SITE FOR RESIDUE PG4 A 957
13
BC4
SOFTWARE
GLY B:406 , THR B:407 , ARG B:408 , HOH B:775
BINDING SITE FOR RESIDUE SO4 B 946
14
BC5
SOFTWARE
ASP B:362 , GLN B:392 , ASN B:394 , THR B:396 , NAG B:605 , HOH B:843
BINDING SITE FOR RESIDUE NAG B 947
15
BC6
SOFTWARE
TYR B:339 , LEU B:359 , VAL B:361 , THR B:398 , NAG B:604 , BMA B:606 , HOH B:853
BINDING SITE FOR RESIDUE NAG B 948
16
BC7
SOFTWARE
TYR B:339 , NAG B:605 , MAN B:607 , MAN B:608
BINDING SITE FOR RESIDUE BMA B 949
17
BC8
SOFTWARE
SER B:341 , BMA B:606
BINDING SITE FOR RESIDUE MAN B 950
18
BC9
SOFTWARE
BMA B:606
BINDING SITE FOR RESIDUE MAN B 951
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_003885 (W478L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_003885
W
359
L
IGHE_HUMAN
Polymorphism
---
A/B
W
478
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (-|A:416-422,B:416-422|A:522-528,B:...)
;
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.
IGHE_HUMAN
83-89
297-303
403-409
4
-
A:416-422
B:416-422
A:522-528
B:522-528
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.2 (A:228-330 | B:225-330)
Exon 1.3 (A:330-438 | B:330-438)
Exon 1.4 (A:438-545 | B:438-546)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/-
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
ENST00000390541
1
ENSE00001935719
chr14:
106068065-106067756
310
IGHE_HUMAN
1-104
104
0
-
-
1.2
ENST00000390541
2
ENSE00001508179
chr14:
106067548-106067228
321
IGHE_HUMAN
104-211
108
2
A:228-330
B:225-330
104
107
1.3
ENST00000390541
3
ENSE00001508174
chr14:
106067141-106066818
324
IGHE_HUMAN
211-319
109
2
A:330-438
B:330-438
109
109
1.4
ENST00000390541
4
ENSE00001943927
chr14:
106066734-106066278
457
IGHE_HUMAN
319-428
110
2
A:438-545
B:438-546
108
109
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2wqra1 (A:228-330)
1b: SCOP_d2wqra2 (A:331-438)
1c: SCOP_d2wqra3 (A:439-545)
1d: SCOP_d2wqrb1 (B:225-330)
1e: SCOP_d2wqrb2 (B:331-438)
1f: SCOP_d2wqrb3 (B:439-546)
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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)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d2wqra1
A:228-330
1b
d2wqra2
A:331-438
1c
d2wqra3
A:439-545
1d
d2wqrb1
B:225-330
1e
d2wqrb2
B:331-438
1f
d2wqrb3
B:439-546
[
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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
(1, 6)
Info
all PFAM domains
1a: PFAM_C1_set_2wqrB01 (B:450-536)
1b: PFAM_C1_set_2wqrB02 (B:450-536)
1c: PFAM_C1_set_2wqrB03 (B:450-536)
1d: PFAM_C1_set_2wqrB04 (B:450-536)
1e: PFAM_C1_set_2wqrB05 (B:450-536)
1f: PFAM_C1_set_2wqrB06 (B:450-536)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-2wqrB01
B:450-536
1b
C1-set-2wqrB02
B:450-536
1c
C1-set-2wqrB03
B:450-536
1d
C1-set-2wqrB04
B:450-536
1e
C1-set-2wqrB05
B:450-536
1f
C1-set-2wqrB06
B:450-536
[
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Protein & NOT PROSITE
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Asymmetric Unit 1
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