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2GTZ
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
HUMAN CLASS I MHC HLA-A2 IN COMPLEX WITH THE NONAMERIC MELAN-A/MART-1(27-35) PEPTIDE HAVING A28L SUBSTITUTION
Authors
:
O. Y. Borbulevych, B. M. Baker
Date
:
28 Apr 06 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Melan-A/Mart-1 Peptide, Nonapeptide, Mhc Class I, Hla-A2, A28L Mutation, Melanoma, Cancer Vaccines, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Y. Borbulevych, F. K. Insaidoo, T. K. Baxter, D. J. Powell, L. A. Johnson, N. P. Restifo, B. M. Baker
Structures Of Mart-1(26/27-35) Peptide/Hla-A2 Complexes Reveal A Remarkable Disconnect Between Antigen Structural Homology And T Cell Recognition
J. Mol. Biol. V. 372 1123 2007
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
6
Ligand/Ion
GLYCEROL
2
NA
2
Ligand/Ion
SODIUM ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN B:83 , HIS B:84 , LEU B:87 , HOH B:5072 , HOH B:5079 , HOH B:5088
BINDING SITE FOR RESIDUE NA B 5001
2
AC2
SOFTWARE
ASN E:83 , HIS E:84 , LEU E:87 , HOH E:5102 , HOH E:5119
BINDING SITE FOR RESIDUE NA E 5002
3
AC3
SOFTWARE
TYR A:84 , ASN A:86 , HIS A:191 , HIS A:192 , ALA A:193 , HOH A:1009 , HOH A:1079 , HOH A:1135 , HOH A:1149
BINDING SITE FOR RESIDUE GOL A 1001
4
AC4
SOFTWARE
ARG A:6 , PHE A:8 , TYR A:27 , ASP A:29 , ASP A:30 , HOH A:1033 , HOH A:1118 , HOH A:1193 , TYR B:63
BINDING SITE FOR RESIDUE GOL A 1002
5
AC5
SOFTWARE
ARG D:6 , ASP D:29 , ASP D:30 , HOH D:1036 , HOH D:1200 , HOH D:1212 , TYR E:63
BINDING SITE FOR RESIDUE GOL D 1003
6
AC6
SOFTWARE
TYR D:84 , ASN D:86 , HIS D:191 , HIS D:192 , ALA D:193 , HOH D:1009 , HOH D:1015 , HOH D:1148 , HOH D:1248
BINDING SITE FOR RESIDUE GOL D 1004
7
AC7
SOFTWARE
GLU A:58 , TYR A:59 , GLY A:62 , GLU A:63 , LYS A:66
BINDING SITE FOR RESIDUE GOL A 1005
8
AC8
SOFTWARE
GLU A:166 , TRP A:167 , ARG A:170
BINDING SITE FOR RESIDUE GOL A 1006
[
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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 (K66N, 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
K
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,A:257-263,D:257-26...)
;
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
1A02_HUMAN
281-287
2
A:257-263
D:257-263
[
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]
Exons
(1, 2)
Info
All Exons
Exon 1.3a (C:1-9 | F:1-9)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2a/1.3a
2: Boundary 1.3a/1.5a
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
ENST00000381477
1a
ENSE00001488744
chr9:
5890802-5890936
135
MAR1_HUMAN
-
0
0
-
-
1.2a
ENST00000381477
2a
ENSE00001488741
chr9:
5892450-5892551
102
MAR1_HUMAN
1-26
26
0
-
-
1.3a
ENST00000381477
3a
ENSE00000813180
chr9:
5897557-5897653
97
MAR1_HUMAN
26-58
33
2
C:1-9
F:1-9
9
9
1.5a
ENST00000381477
5a
ENSE00000927858
chr9:
5906885-5906998
114
MAR1_HUMAN
59-96
38
0
-
-
1.6c
ENST00000381477
6c
ENSE00001488710
chr9:
5908640-5910606
1967
MAR1_HUMAN
97-118
22
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2gtzb_ (B:)
1b: SCOP_d2gtze_ (E:)
2a: SCOP_d2gtza1 (A:182-275)
2b: SCOP_d2gtzd1 (D:182-275)
3a: SCOP_d2gtza2 (A:1-181)
3b: SCOP_d2gtzd2 (D:1-181)
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
d2gtzb_
B:
1b
d2gtze_
E:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d2gtza1
A:182-275
2b
d2gtzd1
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
d2gtza2
A:1-181
3b
d2gtzd2
D:1-181
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2gtzA01 (A:1-181)
1b: CATH_2gtzD01 (D:1-181)
2a: CATH_2gtzB00 (B:0-99)
2b: CATH_2gtzE00 (E:0-99)
2c: CATH_2gtzA02 (A:182-270)
2d: CATH_2gtzD02 (D:182-270)
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)
Human (Homo sapiens)
(249)
1a
2gtzA01
A:1-181
1b
2gtzD01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2gtzB00
B:0-99
2b
2gtzE00
E:0-99
2c
2gtzA02
A:182-270
2d
2gtzD02
D:182-270
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Asym.Unit (153 KB)
Header - Asym.Unit
Biol.Unit 1 (74 KB)
Header - Biol.Unit 1
Biol.Unit 2 (75 KB)
Header - Biol.Unit 2
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