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2IPK
Biol. Unit 1
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Asym.Unit (118 KB)
Biol.Unit 1 (114 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE MHC CLASS II MOLECULE HLA-DR1 IN COMPLEX WITH THE FLUOROGENIC PEPTIDE, ACPKXVKQNTLKLAT (X=3-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]-L-ALANINE) AND THE SUPERANTIGEN, SEC3 VARIANT 3B2
Authors
:
T. T. Nguyen, L. J. Stern
Date
:
12 Oct 06 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hla, Dr1, Mhc, Major Histocompatibility Complex, Fluorogenic Probe, Sec3, 4-(N, N-Dimethylamino) Phthalimidoalanyl, Dapa, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Venkatraman, T. T. Nguyen, M. Sainlos, O. Bilsel, S. Chitta, B. Imperiali, L. J. Stern
Fluorogenic Probes For Monitoring Peptide Binding To Class Ii Mhc Proteins In Living Cells.
Nat. Chem. Biol. V. 3 222 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 3-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3... (4DPa)
2a: ACETYL GROUP (ACEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4DP
1
Mod. Amino Acid
3-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]-L-ALANINE
2
ACE
1
Mod. Amino Acid
ACETYL GROUP
[
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Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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]
SAPs(SNPs)/Variants
(25, 25)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_033379 (R4K, chain B, )
02: VAR_033380 (R4Q, chain B, )
03: VAR_016740 (Q10E, chain B, )
04: VAR_033381 (S37Y, chain B, )
05: VAR_016741 (G45R, chain B, )
06: VAR_033382 (Y47F, chain B, )
07: VAR_033383 (Y60S, chain B, )
08: VAR_016710 (L67I, chain B, )
09: VAR_016711 (Q70D, chain B, )
10: VAR_033384 (Q70E, chain B, )
11: VAR_033385 (Q70H, chain B, )
12: VAR_016742 (R71A, chain B, )
13: VAR_016712 (R71E, chain B, )
14: VAR_033386 (A73G, chain B, )
15: VAR_033387 (A74E, chain B, )
16: VAR_016713 (T77N, chain B, )
17: VAR_033388 (Y78H, chain B, )
18: VAR_016714 (V85A, chain B, )
19: VAR_016715 (G86V, chain B, )
20: VAR_033389 (G135D, chain B, )
21: VAR_033390 (A140T, chain B, )
22: VAR_033391 (V142M, chain B, )
23: VAR_033392 (Q149H, chain B, )
24: VAR_033393 (R166Q, chain B, )
25: VAR_033394 (T181I, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_033379
R
33
K
2B11_HUMAN
Polymorphism
34716432
B
R
4
K
02
UniProt
VAR_033380
R
33
Q
2B11_HUMAN
Polymorphism
34716432
B
R
4
Q
03
UniProt
VAR_016740
Q
39
E
2B11_HUMAN
Polymorphism
---
B
Q
10
E
04
UniProt
VAR_033381
S
66
Y
2B11_HUMAN
Polymorphism
16822820
B
S
37
Y
05
UniProt
VAR_016741
G
74
R
2B11_HUMAN
Polymorphism
---
B
G
45
R
06
UniProt
VAR_033382
Y
76
F
2B11_HUMAN
Polymorphism
1060346
B
Y
47
F
07
UniProt
VAR_033383
Y
89
S
2B11_HUMAN
Polymorphism
36074728
B
Y
60
S
08
UniProt
VAR_016710
L
96
I
2B11_HUMAN
Polymorphism
---
B
L
67
I
09
UniProt
VAR_016711
Q
99
D
2B11_HUMAN
Polymorphism
---
B
Q
70
D
10
UniProt
VAR_033384
Q
99
E
2B11_HUMAN
Polymorphism
17881965
B
Q
70
E
11
UniProt
VAR_033385
Q
99
H
2B11_HUMAN
Polymorphism
17879599
B
Q
70
H
12
UniProt
VAR_016742
R
100
A
2B11_HUMAN
Polymorphism
---
B
R
71
A
13
UniProt
VAR_016712
R
100
E
2B11_HUMAN
Polymorphism
---
B
R
71
E
14
UniProt
VAR_033386
A
102
G
2B11_HUMAN
Polymorphism
17878857
B
A
73
G
15
UniProt
VAR_033387
A
103
E
2B11_HUMAN
Polymorphism
16822805
B
A
74
E
16
UniProt
VAR_016713
T
106
N
2B11_HUMAN
Polymorphism
16822752
B
T
77
N
17
UniProt
VAR_033388
Y
107
H
2B11_HUMAN
Polymorphism
16822512
B
Y
78
H
18
UniProt
VAR_016714
V
114
A
2B11_HUMAN
Polymorphism
17424145
B
V
85
A
19
UniProt
VAR_016715
G
115
V
2B11_HUMAN
Polymorphism
2230810
B
G
86
V
20
UniProt
VAR_033389
G
164
D
2B11_HUMAN
Polymorphism
1059633
B
G
135
D
21
UniProt
VAR_033390
A
169
T
2B11_HUMAN
Polymorphism
2308768
B
A
140
T
22
UniProt
VAR_033391
V
171
M
2B11_HUMAN
Polymorphism
701829
B
V
142
M
23
UniProt
VAR_033392
Q
178
H
2B11_HUMAN
Polymorphism
701830
B
Q
149
H
24
UniProt
VAR_033393
R
195
Q
2B11_HUMAN
Polymorphism
3205588
B
R
166
Q
25
UniProt
VAR_033394
T
210
I
2B11_HUMAN
Polymorphism
17423930
B
T
181
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: STAPH_STREP_TOXIN_1 (D:112-121)
2: STAPH_STREP_TOXIN_2 (D:151-174)
3: IG_MHC (A:161-167)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
STAPH_STREP_TOXIN_1
PS00277
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1.
ENTC3_STAAM
139-148
1
D:112-121
ENTC3_STAAU
139-148
1
D:112-121
2
STAPH_STREP_TOXIN_2
PS00278
Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.
ENTC3_STAAM
178-201
1
D:151-174
ENTC3_STAAU
178-201
1
D:151-174
3
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
DRA_HUMAN
186-192
1
A:161-167
2B11_HUMAN
200-206
1
B:171-177
[
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]
Exons
(0, 0)
Info
All Exons
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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
(6, 6)
Info
All SCOP Domains
1a: SCOP_d2ipka1 (A:83-179)
2a: SCOP_d2ipkb1 (B:93-190)
3a: SCOP_d2ipkd1 (D:1-121)
4a: SCOP_d2ipkd2 (D:122-239)
5a: SCOP_d2ipka2 (A:13-81)
6a: SCOP_d2ipkb2 (B:1-92)
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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
:
Class II MHC alpha chain, C-terminal domain
(75)
Mouse (Mus musculus), I-A group [TaxId: 10090]
(24)
1a
d2ipka1
A:83-179
Protein domain
:
Class II MHC beta chain, C-terminal domain
(70)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(40)
2a
d2ipkb1
B:93-190
Fold
:
OB-fold
(1179)
Superfamily
:
Bacterial enterotoxins
(188)
Family
:
Superantigen toxins, N-terminal domain
(91)
Protein domain
:
Staphylococcal enterotoxin C3, SEC3
(20)
Staphylococcus aureus [TaxId: 1280]
(20)
3a
d2ipkd1
D:1-121
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Superantigen toxins, C-terminal domain
(103)
Family
:
Superantigen toxins, C-terminal domain
(94)
Protein domain
:
Staphylococcal enterotoxin C3, SEC3
(20)
Staphylococcus aureus [TaxId: 1280]
(20)
4a
d2ipkd2
D:122-239
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class II MHC alpha chain, N-terminal domain
(75)
Mouse (Mus musculus), I-AU [TaxId: 10090]
(12)
5a
d2ipka2
A:13-81
Protein domain
:
Class II MHC beta chain, N-terminal domain
(70)
Human (Homo sapiens), HLA-DR4 [TaxId: 9606]
(9)
6a
d2ipkb2
B:1-92
[
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]
CATH Domains
(4, 6)
Info
all CATH domains
1a: CATH_2ipkB01 (B:1-92)
1b: CATH_2ipkA01 (A:3-81)
2a: CATH_2ipkD01 (D:1-31,D:120-237)
3a: CATH_2ipkD02 (D:32-119)
4a: CATH_2ipkA02 (A:82-181)
4b: CATH_2ipkB02 (B:93-190)
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(
)
(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Homologous Superfamily
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Human (Homo sapiens)
(48)
1a
2ipkB01
B:1-92
1b
2ipkA01
A:3-81
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.120, no name defined]
(91)
Human (Homo sapiens)
(21)
2a
2ipkD01
D:1-31,D:120-237
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.110, no name defined]
(136)
Human (Homo sapiens)
(19)
3a
2ipkD02
D:32-119
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
4a
2ipkA02
A:82-181
4b
2ipkB02
B:93-190
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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