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3H9Z
Biol. Unit 2
Info
Asym.Unit (152 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE IGE-FC3-4 DOMAINS
Authors
:
B. A. Wurzburg
Date
:
30 Apr 09 (Deposition) - 08 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Immunoglobin, Ige, Fc, Flexibility, Hydrophobic Pocket, Disulfide Bond, Glycoprotein, Immunoglobulin C Region, Immunoglobulin Domain, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Wurzburg, T. S. Jardetzky
Conformational Flexibility In Immunoglobulin E-Fc 3-4 Revealed In Multiple Crystal Forms.
J. Mol. Biol. V. 393 176 2009
[
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
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: 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)
4a: AMMONIUM ION (NH4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NH4
1
Ligand/Ion
AMMONIUM ION
[
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Sites
(11, 11)
Info
All Sites
01: AC6 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
NAG C:2 , LEU C:363 , ASN C:394 , THR C:396
BINDING SITE FOR RESIDUE NAG C 1
02
AC7
SOFTWARE
NAG C:1 , BMA C:3 , MAN C:4 , TYR C:339 , LEU C:359 , THR C:398
BINDING SITE FOR RESIDUE NAG C 2
03
AC8
SOFTWARE
NAG C:2 , MAN C:4 , MAN C:5
BINDING SITE FOR RESIDUE BMA C 3
04
AC9
SOFTWARE
NAG C:2 , BMA C:3
BINDING SITE FOR RESIDUE MAN C 4
05
BC1
SOFTWARE
BMA C:3
BINDING SITE FOR RESIDUE MAN C 5
06
BC2
SOFTWARE
NAG D:2 , VAL D:361 , ASN D:394 , THR D:396
BINDING SITE FOR RESIDUE NAG D 1
07
BC3
SOFTWARE
NAG D:1 , BMA D:3 , SER D:337 , TYR D:339 , LEU D:359
BINDING SITE FOR RESIDUE NAG D 2
08
BC4
SOFTWARE
NAG D:2 , MAN D:4 , MAN D:5 , TYR D:339
BINDING SITE FOR RESIDUE BMA D 3
09
BC5
SOFTWARE
BMA D:3 , HOH D:133 , GLN D:494
BINDING SITE FOR RESIDUE MAN D 4
10
BC6
SOFTWARE
BMA D:3
BINDING SITE FOR RESIDUE MAN D 5
11
BC7
SOFTWARE
HOH C:210 , SER C:341 , ARG C:342
BINDING SITE FOR RESIDUE NH4 C 548
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_003885 (W478L, chain C/D, )
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
---
C/D
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 (C:416-422,C:522-528,D:522-528)
;
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
-
-
-
C:416-422
D:416-422
-
-
C:522-528
D:522-528
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3h9za1 (A:336-438)
1b: SCOP_d3h9za2 (A:439-544)
1c: SCOP_d3h9zb1 (B:336-438)
1d: SCOP_d3h9zb2 (B:439-544)
1e: SCOP_d3h9zc1 (C:336-438)
1f: SCOP_d3h9zc2 (C:439-544)
1g: SCOP_d3h9zd1 (D:336-438)
1h: SCOP_d3h9zd2 (D:439-544)
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
1a
d3h9za1
A:336-438
1b
d3h9za2
A:439-544
1c
d3h9zb1
B:336-438
1d
d3h9zb2
B:439-544
1e
d3h9zc1
C:336-438
1f
d3h9zc2
C:439-544
1g
d3h9zd1
D:336-438
1h
d3h9zd2
D:439-544
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3h9zA02 (A:436-543)
1b: CATH_3h9zB02 (B:436-543)
1c: CATH_3h9zC02 (C:436-543)
1d: CATH_3h9zD02 (D:436-543)
1e: CATH_3h9zA01 (A:336-435)
1f: CATH_3h9zB01 (B:336-435)
1g: CATH_3h9zC01 (C:336-435)
1h: CATH_3h9zD01 (D:336-435)
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)
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)
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
3h9zA02
A:436-543
1b
3h9zB02
B:436-543
1c
3h9zC02
C:436-543
1d
3h9zD02
D:436-543
1e
3h9zA01
A:336-435
1f
3h9zB01
B:336-435
1g
3h9zC01
C:336-435
1h
3h9zD01
D:336-435
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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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'
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set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
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