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1D6E
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (102 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HLA-DR4 COMPLEX WITH PEPTIDOMIMETIC AND SEB
Authors
:
A. Swain, R. Crowther, U. Kammlott
Date
:
13 Oct 99 (Deposition) - 28 Jun 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mhc Class Ii-Superantigen Complex, Immune System-Peptide Inhibitor Complex, Peptidomimetic Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. R. Bolin, A. L. Swain, R. Sarabu, S. J. Berthel, P. Gillespie, N. J. Huby, R. Makofske, L. Orzechowski, A. Perrotta, K. Toth, J. P. Cooper, N. Jiang, F. Falcioni, R. Campbell, D. Cox, D. Gaizband, C. J. Belunis, D. Vidovic, K. Ito, R. Crowther, U. Kammlott, X. Zhang, R. Palermo, D. Weber, J. Guenot, Z. Nagy, G. L. Olson
Peptide And Peptide Mimetic Inhibitors Of Antigen Presentation By Hla-Dr Class Ii Mhc Molecules. Design, Structure-Activity Relationships, And X-Ray Crystal Structures.
J. Med. Chem. V. 43 2135 2000
[
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Hetero Components
(5, 5)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
2a: 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACI... (ALCa)
3a: N-METHYL-ALPHA-PHENYL-GLYCINE (MPQa)
4a: AMINO GROUP (NH2a)
5a: 3-METHYL-L-VALINE (TBGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
ALC
1
Mod. Amino Acid
2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
3
MPQ
1
Mod. Amino Acid
N-METHYL-ALPHA-PHENYL-GLYCINE
4
NH2
1
Mod. Amino Acid
AMINO GROUP
5
TBG
1
Mod. Amino Acid
3-METHYL-L-VALINE
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:9 , GLU A:11 , PHE A:22 , SER A:53 , PHE A:54 , GLY A:58 , ALA A:59 , ASN A:62 , VAL A:65 , ASP A:66 , ASN A:69 , GLU A:179 , HIS B:13 , TYR B:30 , LYS B:71 , ALA B:74 , THR B:77 , TYR B:78 , HIS B:81 , ASN B:82 , VAL B:85
BINDING SITE FOR CHAIN D OF PROTEIN (PEPTIDOMIMETIC INHIBITOR)
[
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SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016673 (D57S, chain B, )
2: VAR_016674 (L67I, chain B, )
3: VAR_016675 (Q70D, chain B, )
4: VAR_016676 (K71E, chain B, )
5: VAR_016677 (K71R, chain B, )
6: VAR_016678 (A74E, chain B, )
7: VAR_016679 (G86V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016673
D
86
S
2B14_HUMAN
Polymorphism
---
B
D
57
S
2
UniProt
VAR_016674
L
96
I
2B14_HUMAN
Polymorphism
---
B
L
67
I
3
UniProt
VAR_016675
Q
99
D
2B14_HUMAN
Polymorphism
---
B
Q
70
D
4
UniProt
VAR_016676
K
100
E
2B14_HUMAN
Polymorphism
---
B
K
71
E
5
UniProt
VAR_016677
K
100
R
2B14_HUMAN
Polymorphism
---
B
K
71
R
6
UniProt
VAR_016678
A
103
E
2B14_HUMAN
Polymorphism
---
B
A
74
E
7
UniProt
VAR_016679
G
115
V
2B14_HUMAN
Polymorphism
---
B
G
86
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 4)
Info
All PROSITE Patterns/Profiles
1: STAPH_STREP_TOXIN_1 (C:115-124)
2: STAPH_STREP_TOXIN_2 (C:152-175)
3: IG_MHC (A:161-167,B:171-177)
;
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.
ETXB_STAAU
142-151
1
C:115-124
2
STAPH_STREP_TOXIN_2
PS00278
Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.
ETXB_STAAU
179-202
1
C:152-175
3
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
DRA_HUMAN
186-192
1
A:161-167
2B14_HUMAN
200-206
1
B:171-177
[
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Exons
(3, 3)
Info
All Exons
Exon 1.7b (A:4-85)
Exon 1.8c (A:85-179)
Exon 1.9a (A:179-180)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.6a/1.7b
2: Boundary 1.7b/1.8c
3: Boundary 1.8c/1.9a
4: Boundary 1.9a/1.10b
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
1.6a
ENST00000383259
6a
ENSE00001839042
HSCHR6_MHC_QBL:32365090-32365280
191
DRA_HUMAN
1-28
28
0
-
-
1.7b
ENST00000383259
7b
ENSE00001719010
HSCHR6_MHC_QBL:32367694-32367939
246
DRA_HUMAN
28-110
83
1
A:4-85
82
1.8c
ENST00000383259
8c
ENSE00001737588
HSCHR6_MHC_QBL:32368431-32368712
282
DRA_HUMAN
110-204
95
1
A:85-179
95
1.9a
ENST00000383259
9a
ENSE00001770912
HSCHR6_MHC_QBL:32369002-32369167
166
DRA_HUMAN
204-254
51
1
A:179-180
2
1.10b
ENST00000383259
10b
ENSE00001925700
HSCHR6_MHC_QBL:32369906-32370300
395
DRA_HUMAN
-
0
0
-
-
[
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SCOP Domains
(6, 6)
Info
All SCOP Domains
1a: SCOP_d1d6ea1 (A:82-180)
2a: SCOP_d1d6eb1 (B:93-190)
3a: SCOP_d1d6ec1 (C:2-121)
4a: SCOP_d1d6ec2 (C:122-237)
5a: SCOP_d1d6ea2 (A:4-81)
6a: SCOP_d1d6eb2 (B:3-92)
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)
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Folds
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)
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)
(
)
Families
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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
:
Class II MHC alpha chain, C-terminal domain
(75)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(37)
1a
d1d6ea1
A:82-180
Protein domain
:
Class II MHC beta chain, C-terminal domain
(70)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(40)
2a
d1d6eb1
B:93-190
Fold
:
OB-fold
(1179)
Superfamily
:
Bacterial enterotoxins
(188)
Family
:
Superantigen toxins, N-terminal domain
(91)
Protein domain
:
Staphylococcal enterotoxin B, SEB
(14)
Staphylococcus aureus [TaxId: 1280]
(14)
3a
d1d6ec1
C:2-121
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 B, SEB
(14)
Staphylococcus aureus [TaxId: 1280]
(14)
4a
d1d6ec2
C:122-237
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)
Human (Homo sapiens), HLA-DR4 [TaxId: 9606]
(5)
5a
d1d6ea2
A:4-81
Protein domain
:
Class II MHC beta chain, N-terminal domain
(70)
Human (Homo sapiens), HLA-DR4 [TaxId: 9606]
(9)
6a
d1d6eb2
B:3-92
[
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CATH Domains
(4, 6)
Info
all CATH domains
1a: CATH_1d6eB01 (B:3-91)
1b: CATH_1d6eA01 (A:4-81)
2a: CATH_1d6eC02 (C:2-31,C:128-231)
3a: CATH_1d6eC01 (C:32-121)
4a: CATH_1d6eA02 (A:82-180)
4b: CATH_1d6eB02 (B:92-190)
View:
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(
)
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
1d6eB01
B:3-91
1b
1d6eA01
A:4-81
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.120, no name defined]
(91)
Human (Homo sapiens)
(21)
2a
1d6eC02
C:2-31,C:128-231
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
1d6eC01
C:32-121
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
4a
1d6eA02
A:82-180
4b
1d6eB02
B:92-190
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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