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2AV1
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HTLV-1 TAX PEPTIDE BOUND TO HUMAN CLASS I MHC HLA-A2 WITH THE E63Q AND K66A MUTATIONS IN THE HEAVY CHAIN.
Authors
:
O. Y. Borbulevych, B. M. Baker
Date
:
29 Aug 05 (Deposition) - 18 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Tax Peptide, Mhc, Mutated Hla-A2, E63Q, K66A, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. J. Gagnon, O. Y. Borbulevych, R. L. Davis-Harrison, T. K. Baxter, J. R. Clemens, K. M. Armstrong, R. V. Turner, M. Damirjian, W. E. Biddison, B. M. Baker
Unraveling A Hotspot For Tcr Recognition On Hla-A2: Evidenc Against The Existence Of Peptide-Independent Tcr Binding Determinants.
J. Mol. Biol. V. 353 556 2005
[
close entry info
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
1w: GLYCEROL (GOLw)
2a: THIOCYANATE ION (SCNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
23
Ligand/Ion
GLYCEROL
2
SCN
1
Ligand/Ion
THIOCYANATE ION
[
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Sites
(24, 24)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR B:86 , ASP D:220 , ARG D:256 , ASN E:42
BINDING SITE FOR RESIDUE SCN B 801
02
AC2
SOFTWARE
HIS D:188 , TRP D:204 , LEU D:206 , ARG D:234 , GLN D:242 , SER E:11 , HIS E:13 , PRO E:14 , HOH E:918
BINDING SITE FOR RESIDUE GOL E 901
03
AC3
SOFTWARE
VAL A:231 , ARG A:234 , TRP A:244 , HOH A:944 , HOH A:977 , HOH A:1144 , GLN B:8 , MET B:99 , HOH B:954
BINDING SITE FOR RESIDUE GOL A 902
04
AC4
SOFTWARE
LEU B:40 , LYS B:41 , ASN B:42 , GLY B:43 , GLU B:77 , TYR B:78 , ALA B:79 , HOH B:969
BINDING SITE FOR RESIDUE GOL B 903
05
AC5
SOFTWARE
ARG D:111 , GLY D:112 , TYR D:113 , LEU D:126 , LYS D:127 , GLU D:128
BINDING SITE FOR RESIDUE GOL D 904
06
AC6
SOFTWARE
ARG D:44 , MET D:45 , TRP D:60
BINDING SITE FOR RESIDUE GOL D 905
07
AC7
SOFTWARE
GLU A:232 , SER B:57 , LYS B:58 , ASP B:59 , HOH B:984
BINDING SITE FOR RESIDUE GOL B 906
08
AC8
SOFTWARE
ASP A:106 , TRP A:107 , ARG A:169 , HOH A:938 , HOH A:1039 , ARG D:131 , GLU D:154
BINDING SITE FOR RESIDUE GOL A 907
09
AC9
SOFTWARE
GLN A:155 , TYR A:159 , THR A:163 , PHE C:3 , GLY C:4 , TYR C:5 , HOH C:101
BINDING SITE FOR RESIDUE GOL C 908
10
BC1
SOFTWARE
LEU A:206 , ARG A:234 , GLN A:242 , TYR B:10 , SER B:11 , HIS B:13 , PRO B:14 , HOH B:943 , HOH B:977
BINDING SITE FOR RESIDUE GOL B 909
11
BC2
SOFTWARE
GLY A:104 , ASP A:106 , ARG A:108 , PHE A:109 , LEU A:110 , HOH A:991 , HOH A:997
BINDING SITE FOR RESIDUE GOL A 910
12
BC3
SOFTWARE
SER E:57 , LYS E:58 , ASP E:59
BINDING SITE FOR RESIDUE GOL E 911
13
BC4
SOFTWARE
TRP A:167 , ARG A:170 , HOH A:1004 , HOH E:958
BINDING SITE FOR RESIDUE GOL A 912
14
BC5
SOFTWARE
SER A:207 , THR A:240 , ASP D:61
BINDING SITE FOR RESIDUE GOL A 913
15
BC6
SOFTWARE
HIS D:191 , ALA D:193 , SER D:195 , ASP D:196 , GLU D:198 , GLU D:254 , HOH D:1109 , HOH D:1143
BINDING SITE FOR RESIDUE GOL D 914
16
BC7
SOFTWARE
ASP A:61 , SER D:207 , ALA D:236 , ASP D:238 , THR D:240 , HOH D:923 , ARG E:12 , HIS E:13
BINDING SITE FOR RESIDUE GOL D 915
17
BC8
SOFTWARE
TYR D:27 , GLN D:32 , SER E:52 , TYR E:63 , HOH E:973
BINDING SITE FOR RESIDUE GOL E 916
18
BC9
SOFTWARE
GLN D:224 , ASP D:227 , VAL D:248 , TYR D:257 , HOH D:977 , HOH D:1061
BINDING SITE FOR RESIDUE GOL D 917
19
CC1
SOFTWARE
SER B:20 , GLU D:58 , TYR D:59 , TRP D:167 , HOH D:992 , HOH D:1052
BINDING SITE FOR RESIDUE GOL D 918
20
CC2
SOFTWARE
ARG B:3 , THR B:4 , LYS B:6 , HOH B:966 , HIS D:197 , PRO D:250 , SER D:251 , GLN D:253
BINDING SITE FOR RESIDUE GOL B 919
21
CC3
SOFTWARE
TYR A:27 , ASP A:29 , ASP A:30 , HOH A:989 , TYR B:63
BINDING SITE FOR RESIDUE GOL A 920
22
CC4
SOFTWARE
PRO A:235 , TYR B:26 , SER B:52 , TYR B:63 , HOH B:926 , HOH B:992 , HOH B:1008 , HOH B:1037
BINDING SITE FOR RESIDUE GOL B 921
23
CC5
SOFTWARE
SER D:13 , ARG D:14 , GLY D:18 , GLU D:19 , PRO D:20 , HOH D:976 , HOH D:1140
BINDING SITE FOR RESIDUE GOL D 922
24
CC6
SOFTWARE
ASN B:83 , HIS B:84 , VAL B:85 , LEU B:87 , SER B:88 , HOH B:1004
BINDING SITE FOR RESIDUE GOL B 923
[
close Site info
]
SAPs(SNPs)/Variants
(22, 44)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004334 (F9Y, chain A/D, )
02: VAR_004335 (D30N, chain A/D, )
03: VAR_016726 (A41G, chain A/D, )
04: VAR_004336 (Q43R, chain A/D, )
05: VAR_004337 (A66N, chain A/D, )
06: VAR_016727 (H70Q, chain A/D, )
07: VAR_004338 (T73I, chain A/D, )
08: VAR_016728 (H74D, chain A/D, )
09: VAR_004339 (V95L, chain A/D, )
10: VAR_004340 (R97M, chain A/D, )
11: VAR_004341 (Y99C, chain A/D, )
12: VAR_004342 (Y99F, chain A/D, )
13: VAR_004343 (W107G, chain A/D, )
14: VAR_004344 (M138K, chain A/D, )
15: VAR_004345 (A149T, chain A/D, )
16: VAR_004346 (V152E, chain A/D, )
17: VAR_004348 (L156Q, chain A/D, )
18: VAR_004347 (L156W, chain A/D, )
19: VAR_004349 (T163E, chain A/D, )
20: VAR_016729 (E166D, chain A/D, )
21: VAR_016730 (W167G, chain A/D, )
22: VAR_004350 (A236E, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004334
F
33
Y
1A02_HUMAN
Polymorphism
---
A/D
F
9
Y
02
UniProt
VAR_004335
D
54
N
1A02_HUMAN
Polymorphism
---
A/D
D
30
N
03
UniProt
VAR_016726
A
65
G
1A02_HUMAN
Polymorphism
---
A/D
A
41
G
04
UniProt
VAR_004336
Q
67
R
1A02_HUMAN
Polymorphism
---
A/D
Q
43
R
05
UniProt
VAR_004337
K
90
N
1A02_HUMAN
Polymorphism
---
A/D
A
66
N
06
UniProt
VAR_016727
H
94
Q
1A02_HUMAN
Polymorphism
---
A/D
H
70
Q
07
UniProt
VAR_004338
T
97
I
1A02_HUMAN
Polymorphism
---
A/D
T
73
I
08
UniProt
VAR_016728
H
98
D
1A02_HUMAN
Polymorphism
---
A/D
H
74
D
09
UniProt
VAR_004339
V
119
L
1A02_HUMAN
Polymorphism
---
A/D
V
95
L
10
UniProt
VAR_004340
R
121
M
1A02_HUMAN
Polymorphism
---
A/D
R
97
M
11
UniProt
VAR_004341
Y
123
C
1A02_HUMAN
Polymorphism
---
A/D
Y
99
C
12
UniProt
VAR_004342
Y
123
F
1A02_HUMAN
Polymorphism
---
A/D
Y
99
F
13
UniProt
VAR_004343
W
131
G
1A02_HUMAN
Polymorphism
---
A/D
W
107
G
14
UniProt
VAR_004344
M
162
K
1A02_HUMAN
Polymorphism
---
A/D
M
138
K
15
UniProt
VAR_004345
A
173
T
1A02_HUMAN
Polymorphism
---
A/D
A
149
T
16
UniProt
VAR_004346
V
176
E
1A02_HUMAN
Polymorphism
---
A/D
V
152
E
17
UniProt
VAR_004348
L
180
Q
1A02_HUMAN
Polymorphism
---
A/D
L
156
Q
18
UniProt
VAR_004347
L
180
W
1A02_HUMAN
Polymorphism
---
A/D
L
156
W
19
UniProt
VAR_004349
T
187
E
1A02_HUMAN
Polymorphism
---
A/D
T
163
E
20
UniProt
VAR_016729
E
190
D
1A02_HUMAN
Polymorphism
---
A/D
E
166
D
21
UniProt
VAR_016730
W
191
G
1A02_HUMAN
Polymorphism
---
A/D
W
167
G
22
UniProt
VAR_004350
A
260
E
1A02_HUMAN
Polymorphism
---
A/D
A
236
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,E:78-84,B:78-84,E:78-84,A:...)
;
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
E:78-84
B2MG_PANTR
98-104
2
B:78-84
E:78-84
1A02_HUMAN
281-287
2
A:257-263
D:257-263
[
close PROSITE info
]
Exons
(3, 6)
Info
All Exons
Exon 1.1a (B:0-3 | E:0-3)
Exon 1.2a (B:3-96 | E:3-96)
Exon 1.4 (B:96-99 | E:96-99)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2a
3: Boundary 1.2a/1.4
4: Boundary 1.4/1.5
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
1.1a
ENSPTRT00000012956
1a
ENSPTRE00000370636
chr15:
41860468-41860604
137
B2MG_PANTR
1-23
23
2
B:0-3
E:0-3
4
4
1.2a
ENSPTRT00000012956
2a
ENSPTRE00000238527
chr15:
41864413-41864691
279
B2MG_PANTR
23-116
94
2
B:3-96
E:3-96
94
94
1.4
ENSPTRT00000012956
4
ENSPTRE00000238528
chr15:
41865318-41865345
28
B2MG_PANTR
116-119
4
2
B:96-99
E:96-99
4
4
1.5
ENSPTRT00000012956
5
ENSPTRE00000070423
chr15:
41866598-41867140
543
B2MG_PANTR
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2av1b_ (B:)
1b: SCOP_d2av1e_ (E:)
2a: SCOP_d2av1a1 (A:182-275)
2b: SCOP_d2av1d1 (D:182-275)
3a: SCOP_d2av1a2 (A:1-181)
3b: SCOP_d2av1d2 (D:1-181)
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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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d2av1b_
B:
1b
d2av1e_
E:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d2av1a1
A:182-275
2b
d2av1d1
D:182-275
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, alpha-1 and alpha-2 domains
(294)
Human (Homo sapiens), HLA-A2.1 [TaxId: 9606]
(92)
3a
d2av1a2
A:1-181
3b
d2av1d2
D:1-181
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2av1A01 (A:1-181)
1b: CATH_2av1D01 (D:1-181)
2a: CATH_2av1B00 (B:0-99)
2b: CATH_2av1A02 (A:182-270)
2c: CATH_2av1D02 (D:182-270)
2d: CATH_2av1E00 (E:0-99)
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Topologies
(
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(
)
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)
Human (Homo sapiens)
(249)
1a
2av1A01
A:1-181
1b
2av1D01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2av1B00
B:0-99
2b
2av1A02
A:182-270
2c
2av1D02
D:182-270
2d
2av1E00
E:0-99
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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