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1YPZ
Asym. Unit
Info
Asym.Unit (277 KB)
Biol.Unit 1 (268 KB)
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(1)
Title
:
IMMUNE RECEPTOR
Authors
:
E. J. Adams, K. C. Garcia
Date
:
31 Jan 05 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
H2-T22 Protein, Beta-2-Microglobulin, T Cell Receptor Delta, T-Cell Receptor Gamma Chain, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. J. Adams, Y. H. Chien, K. C. Garcia
Structure Of A Gammadelta T Cell Receptor In Complex With The Nonclassical Mhc T22.
Science V. 308 227 2005
[
close entry info
]
Hetero Components
(3, 13)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
2
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN E:133 , NAG E:209 , THR F:133 , ILE F:134 , LEU F:136
BINDING SITE FOR RESIDUE NAG E 208
02
AC2
SOFTWARE
NAG E:208 , MAN E:210
BINDING SITE FOR RESIDUE NAG E 209
03
AC3
SOFTWARE
NAG E:209 , PHE F:224
BINDING SITE FOR RESIDUE MAN E 210
04
AC4
SOFTWARE
GLU E:5 , ASN E:24 , TYR E:70 , NAG E:212
BINDING SITE FOR RESIDUE NAG E 211
05
AC5
SOFTWARE
ARG E:22 , NAG E:211 , ASP G:18
BINDING SITE FOR RESIDUE NAG E 212
06
AC6
SOFTWARE
THR F:185 , ASN F:186 , ASP F:187 , NAG F:232
BINDING SITE FOR RESIDUE NAG F 231
07
AC7
SOFTWARE
NAG F:231
BINDING SITE FOR RESIDUE NAG F 232
08
AC8
SOFTWARE
ASN G:133 , NAG G:209 , THR H:133 , ILE H:134
BINDING SITE FOR RESIDUE NAG G 208
09
AC9
SOFTWARE
NAG G:208 , MAN G:210
BINDING SITE FOR RESIDUE NAG G 209
10
BC1
SOFTWARE
NAG G:209 , PHE H:224
BINDING SITE FOR RESIDUE MAN G 210
11
BC2
SOFTWARE
NAG G:212 , NAG G:213
BINDING SITE FOR RESIDUE FUC G 211
12
BC3
SOFTWARE
GLU G:5 , ASN G:24 , FUC G:211 , NAG G:213
BINDING SITE FOR RESIDUE NAG G 212
13
BC4
SOFTWARE
FUC G:211 , NAG G:212
BINDING SITE FOR RESIDUE NAG G 213
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076691 (D76N, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_076691
D
96
N
B2MG_HUMAN
Disease (AMYL8)
398122820
B/D
D
76
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,D:78-84)
;
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.
B2MG_HUMAN
98-104
2
B:78-84
D:78-84
[
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Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(7, 14)
Info
All SCOP Domains
1a: SCOP_d1ypzb1 (B:1-99)
1b: SCOP_d1ypzd1 (D:1-99)
2a: SCOP_d1ypza1 (A:181-276)
2b: SCOP_d1ypzc1 (C:181-276)
3a: SCOP_d1ypze2 (E:120-207)
3b: SCOP_d1ypzg2 (G:120-207)
4a: SCOP_d1ypzf2 (F:121-230)
4b: SCOP_d1ypzh2 (H:121-230)
5a: SCOP_d1ypze1 (E:1-119)
5b: SCOP_d1ypzg1 (G:1-119)
6a: SCOP_d1ypzf1 (F:1-120)
6b: SCOP_d1ypzh1 (H:1-120)
7a: SCOP_d1ypza2 (A:1-180)
7b: SCOP_d1ypzc2 (C:1-180)
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
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1ypzb1
B:1-99
1b
d1ypzd1
D:1-99
Protein domain
:
Class I MHC homolog, alpha-3 domain
(6)
Mouse (Mus musculus), t22 [TaxId: 10090]
(2)
2a
d1ypza1
A:181-276
2b
d1ypzc1
C:181-276
Protein domain
:
T-cell antigen receptor
(81)
Human (Homo sapiens), delta-chain [TaxId: 9606]
(2)
3a
d1ypze2
E:120-207
3b
d1ypzg2
G:120-207
Human (Homo sapiens), gamma-chain [TaxId: 9606]
(2)
4a
d1ypzf2
F:121-230
4b
d1ypzh2
H:121-230
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
T-cell antigen receptor
(105)
Human (Homo sapiens), delta-chain [TaxId: 9606]
(3)
5a
d1ypze1
E:1-119
5b
d1ypzg1
G:1-119
Human (Homo sapiens), gamma-chain [TaxId: 9606]
(3)
6a
d1ypzf1
F:1-120
6b
d1ypzh1
H:1-120
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC homolog
(6)
Mouse (Mus musculus), t22 [TaxId: 10090]
(2)
7a
d1ypza2
A:1-180
7b
d1ypzc2
C:1-180
[
close SCOP info
]
CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_1ypzA01 (A:1-179)
1b: CATH_1ypzC01 (C:1-179)
2a: CATH_1ypzB00 (B:-2-99)
2b: CATH_1ypzA02 (A:180-276)
2c: CATH_1ypzC02 (C:180-276)
2d: CATH_1ypzD00 (D:-2-99)
2e: CATH_1ypzE01 (E:1-120)
2f: CATH_1ypzG01 (G:1-120)
2g: CATH_1ypzF02 (F:124-230)
2h: CATH_1ypzH02 (H:124-230)
2i: CATH_1ypzE02 (E:121-207)
2j: CATH_1ypzG02 (G:121-207)
2k: CATH_1ypzF01 (F:1-123)
2l: CATH_1ypzH01 (H:1-123)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
House mouse (Mus musculus)
(92)
1a
1ypzA01
A:1-179
1b
1ypzC01
C:1-179
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
2a
1ypzB00
B:-2-99
2b
1ypzA02
A:180-276
2c
1ypzC02
C:180-276
2d
1ypzD00
D:-2-99
2e
1ypzE01
E:1-120
2f
1ypzG01
G:1-120
2g
1ypzF02
F:124-230
2h
1ypzH02
H:124-230
2i
1ypzE02
E:121-207
2j
1ypzG02
G:121-207
2k
1ypzF01
F:1-123
2l
1ypzH01
H:1-123
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_C1_set_1ypzD01 (D:11-92)
1b: PFAM_C1_set_1ypzD02 (D:11-92)
2a: PFAM_C1_set_1ypzC01 (C:189-271)
2b: PFAM_C1_set_1ypzC02 (C:189-271)
3a: PFAM_MHC_I_1ypzC03 (C:1-179)
3b: PFAM_MHC_I_1ypzC04 (C:1-179)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1ypzD01
D:11-92
1b
C1-set-1ypzD02
D:11-92
Mus musculus (Mouse)
(118)
2a
C1-set-1ypzC01
C:189-271
2b
C1-set-1ypzC02
C:189-271
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Mus musculus (Mouse)
(60)
3a
MHC_I-1ypzC03
C:1-179
3b
MHC_I-1ypzC04
C:1-179
[
close Pfam info
]
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Asym.Unit (277 KB)
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