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1NFD
Biol. Unit 3
Info
Asym.Unit (290 KB)
Biol.Unit 1 (145 KB)
Biol.Unit 2 (144 KB)
Biol.Unit 3 (216 KB)
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(1)
Title
:
AN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH AN ANTI-TCR FAB FRAGMENT DERIVED FROM A MITOGENIC ANTIBODY
Authors
:
J. -H. Wang, K. Lim, A. Smolyar, M. -K. Teng, J. Sacchittini, E. L. Reinhe
Date
:
04 Aug 97 (Deposition) - 28 Jan 98 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: C,D,G,H (1x)
Biol. Unit 2: A,B,E,F (1x)
Biol. Unit 3: A,B,C,D,E,F (1x)
Keywords
:
Complex (Immunoreceptor-Immunoglobulin), Complex (Immunoreceptor- Immunoglobulin) Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Wang, K. Lim, A. Smolyar, M. Teng, J. Liu, A. G. Tse, J. Liu, R. E. Hussey, Y. Chishti, C. T. Thomson, R. M. Sweet, S. G. Nathenson, H. C. Chang, J. C. Sacchettini, E. L. Reinherz
Atomic Structure Of An Alphabeta T Cell Receptor (Tcr) Heterodimer In Complex With An Anti-Tcr Fab Fragment Derive From A Mitogenic Antibody.
Embo J. V. 17 10 1998
(for further references see the
PDB file header
)
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
2b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
2c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
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Sites
(14, 14)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:6 , LYS A:19 , ASN A:21
BINDING SITE FOR RESIDUE NAG A 214
02
AC2
SOFTWARE
ASN A:185 , GLN A:186 , VAL E:146 , THR E:147 , ASN E:156
BINDING SITE FOR RESIDUE NAG A 215
03
AC3
SOFTWARE
ASN A:203 , ILE E:5 , PRO E:7 , THR E:22 , CYS E:23 , SER E:24
BINDING SITE FOR RESIDUE NAG A 216
04
AC4
SOFTWARE
ARG B:18 , ASN B:78
BINDING SITE FOR RESIDUE NDG B 248
05
AC5
SOFTWARE
ASP B:118 , ASN B:121 , PHE F:98
BINDING SITE FOR RESIDUE NAG B 249
06
AC6
SOFTWARE
ASN B:186 , TYR B:187
BINDING SITE FOR RESIDUE NAG B 250
07
AC7
SOFTWARE
GLN B:213 , GLN B:215 , ASN B:236
BINDING SITE FOR RESIDUE NAG B 251
08
AC8
SOFTWARE
THR C:6 , ASN C:21
BINDING SITE FOR RESIDUE NDG C 214
09
AC9
SOFTWARE
GLY C:159 , ASN C:185
BINDING SITE FOR RESIDUE NDG C 215
10
BC1
SOFTWARE
PRO C:123 , ASN C:203 , ALA C:204
BINDING SITE FOR RESIDUE NAG C 216
11
BC2
SOFTWARE
ARG D:18 , ASN D:78
BINDING SITE FOR RESIDUE NAG D 248
12
BC3
SOFTWARE
ASP D:118 , ASN D:121 , TYR D:187 , PHE H:98
BINDING SITE FOR RESIDUE NAG D 249
13
BC4
SOFTWARE
LYS D:180 , ASN D:186 , TYR D:187
BINDING SITE FOR RESIDUE NAG D 250
14
BC5
SOFTWARE
ARG D:211 , GLN D:213 , ASN D:236
BINDING SITE FOR RESIDUE NAG D 251
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_TCB1_MOUSE_001 (Y190H, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_TCB1_MOUSE_001
*
Y
70
H
TCB1_MOUSE
---
---
B/D
Y
190
H
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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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
(8, 16)
Info
All SCOP Domains
1a: SCOP_d1nfdf2 (F:115-228)
1b: SCOP_d1nfdh2 (H:115-228)
2a: SCOP_d1nfde2 (E:108-215)
2b: SCOP_d1nfdg2 (G:108-215)
3a: SCOP_d1nfda2 (A:118-213)
3b: SCOP_d1nfdc2 (C:118-213)
4a: SCOP_d1nfdb2 (B:118-247)
4b: SCOP_d1nfdd2 (D:118-247)
5a: SCOP_d1nfdf1 (F:1-114)
5b: SCOP_d1nfdh1 (H:1-114)
6a: SCOP_d1nfde1 (E:2-107)
6b: SCOP_d1nfdg1 (G:2-107)
7a: SCOP_d1nfda1 (A:1-117)
7b: SCOP_d1nfdc1 (C:1-117)
8a: SCOP_d1nfdb1 (B:1-117)
8b: SCOP_d1nfdd1 (D:1-117)
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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
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Chinese hamster (Cricetulus griseus) [TaxId: 10029]
(1)
1a
d1nfdf2
F:115-228
1b
d1nfdh2
H:115-228
Protein domain
:
Immunoglobulin light chain lambda constant domain, CL-lambda
(68)
Chinese hamster (Cricetulus griseus) [TaxId: 10029]
(1)
2a
d1nfde2
E:108-215
2b
d1nfdg2
G:108-215
Protein domain
:
T-cell antigen receptor
(81)
Mouse (Mus musculus), alpha-chain [TaxId: 10090]
(11)
3a
d1nfda2
A:118-213
3b
d1nfdc2
C:118-213
Mouse (Mus musculus), beta-chain [TaxId: 10090]
(15)
4a
d1nfdb2
B:118-247
4b
d1nfdd2
D:118-247
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Chinese hamster (Cricetulus griseus) [TaxId: 10029]
(1)
5a
d1nfdf1
F:1-114
5b
d1nfdh1
H:1-114
Protein domain
:
Immunoglobulin light chain lambda variable domain, VL-lambda
(89)
Chinese hamster (Cricetulus griseus) [TaxId: 10029]
(1)
6a
d1nfde1
E:2-107
6b
d1nfdg1
G:2-107
Protein domain
:
T-cell antigen receptor
(105)
Mouse (Mus musculus), alpha-chain [TaxId: 10090]
(21)
7a
d1nfda1
A:1-117
7b
d1nfdc1
C:1-117
Mouse (Mus musculus), beta-chain [TaxId: 10090]
(28)
8a
d1nfdb1
B:1-117
8b
d1nfdd1
D:1-117
[
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]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_1nfdF02 (F:114-226)
1b: CATH_1nfdH02 (H:114-226)
1c: CATH_1nfdE01 (E:2-107)
1d: CATH_1nfdG01 (G:2-107)
1e: CATH_1nfdB01 (B:3-117)
1f: CATH_1nfdD01 (D:3-117)
1g: CATH_1nfdE02 (E:108-215)
1h: CATH_1nfdG02 (G:108-215)
1i: CATH_1nfdF01 (F:1-113)
1j: CATH_1nfdH01 (H:1-113)
1k: CATH_1nfdA02 (A:117-213)
1l: CATH_1nfdC02 (C:117-213)
1m: CATH_1nfdB02 (B:118-246)
1n: CATH_1nfdD02 (D:118-246)
1o: CATH_1nfdA01 (A:1-116)
1p: CATH_1nfdC01 (C:1-116)
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)
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)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
1a
1nfdF02
F:114-226
1b
1nfdH02
H:114-226
1c
1nfdE01
E:2-107
1d
1nfdG01
G:2-107
1e
1nfdB01
B:3-117
1f
1nfdD01
D:3-117
1g
1nfdE02
E:108-215
1h
1nfdG02
G:108-215
1i
1nfdF01
F:1-113
1j
1nfdH01
H:1-113
1k
1nfdA02
A:117-213
1l
1nfdC02
C:117-213
1m
1nfdB02
B:118-246
1n
1nfdD02
D:118-246
1o
1nfdA01
A:1-116
1p
1nfdC01
C:1-116
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_C1_set_1nfdD01 (D:131-224)
1b: PFAM_C1_set_1nfdD02 (D:131-224)
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)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Mus musculus (Mouse)
(118)
1a
C1-set-1nfdD01
D:131-224
1b
C1-set-1nfdD02
D:131-224
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Asym.Unit (290 KB)
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Biol.Unit 1 (145 KB)
Header - Biol.Unit 1
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Biol.Unit 3 (216 KB)
Header - Biol.Unit 3
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