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3S5L
Asym. Unit
Info
Asym.Unit (193 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (96 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD4 MUTANT BOUND TO HLA-DR1
Authors
:
Y. Li
Date
:
23 May 11 (Deposition) - 21 Sep 11 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,G (1x)
Biol. Unit 2: D,E,F,H (1x)
Keywords
:
Protein-Protein Complex, Immune System, Co-Receptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. X. Wang, Y. Li, Y. Yin, M. Mo, Q. Wang, W. Gao, L. Wang, R. A. Mariuzza
Affinity Maturation Of Human Cd4 By Yeast Surface Display And Crystal Structure Of A Cd4-Hla-Dr1 Complex.
Proc. Natl. Acad. Sci. Usa V. 108 15960 2011
[
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Hetero Components
(1, 10)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
10
Ligand/Ion
GLYCEROL
[
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:44 , ASN A:94 , VAL A:104 , TYR A:150 , HOH A:244 , ASP B:152
BINDING SITE FOR RESIDUE GOL A 968
02
AC2
SOFTWARE
ARG D:44 , VAL D:104 , TYR D:150 , ASP E:152
BINDING SITE FOR RESIDUE GOL D 961
03
AC3
SOFTWARE
ILE B:127 , GLU B:128 , VAL B:129 , SER B:144 , GLY B:146 , THR B:157
BINDING SITE FOR RESIDUE GOL B 966
04
AC4
SOFTWARE
SER B:126 , GLU B:128 , GLU B:176 , HIS B:177 , PRO B:178 , HOH B:267
BINDING SITE FOR RESIDUE GOL B 969
05
AC5
SOFTWARE
SER E:126 , ILE E:127 , GLU E:128 , GLU E:176 , HIS E:177 , PRO E:178
BINDING SITE FOR RESIDUE GOL E 960
06
AC6
SOFTWARE
LEU E:114 , GLU E:162 , GLN H:25 , LYS H:35 , ASN H:39 , TRP H:45
BINDING SITE FOR RESIDUE GOL E 962
07
AC7
SOFTWARE
VAL E:129 , SER E:144 , GLY E:146 , THR E:157
BINDING SITE FOR RESIDUE GOL E 963
08
AC8
SOFTWARE
ARG G:58 , ARG G:60
BINDING SITE FOR RESIDUE GOL G 965
09
AC9
SOFTWARE
GLU B:162 , LYS G:35 , ASN G:39 , TRP G:45
BINDING SITE FOR RESIDUE GOL G 967
10
BC1
SOFTWARE
HOH D:220 , ARG H:58 , ARG H:60
BINDING SITE FOR RESIDUE GOL H 964
[
close Site info
]
SAPs(SNPs)/Variants
(27, 54)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_033378 (M0S, chain B/E, )
02: VAR_033379 (R4K, chain B/E, )
03: VAR_033380 (R4Q, chain B/E, )
04: VAR_016740 (Q10E, chain B/E, )
05: VAR_033381 (S37Y, chain B/E, )
06: VAR_016741 (G45R, chain B/E, )
07: VAR_033382 (Y47F, chain B/E, )
08: VAR_033383 (Y60S, chain B/E, )
09: VAR_016710 (L67I, chain B/E, )
10: VAR_016711 (Q70D, chain B/E, )
11: VAR_033384 (Q70E, chain B/E, )
12: VAR_033385 (Q70H, chain B/E, )
13: VAR_016742 (R71A, chain B/E, )
14: VAR_016712 (R71E, chain B/E, )
15: VAR_033386 (A73G, chain B/E, )
16: VAR_033387 (A74E, chain B/E, )
17: VAR_016713 (T77N, chain B/E, )
18: VAR_033388 (Y78H, chain B/E, )
19: VAR_016714 (V85A, chain B/E, )
20: VAR_016715 (G86V, chain B/E, )
21: VAR_033389 (G135D, chain B/E, )
22: VAR_033390 (A140T, chain B/E, )
23: VAR_033391 (V142M, chain B/E, )
24: VAR_033392 (Q149H, chain B/E, )
25: VAR_023459 (K166E, chain G/H, )
26: VAR_033393 (R166Q, chain B/E, )
27: VAR_033394 (T181I, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_033378
A
29
S
2B11_HUMAN
Polymorphism
9270299
B/E
M
0
S
02
UniProt
VAR_033379
R
33
K
2B11_HUMAN
Polymorphism
34716432
B/E
R
4
K
03
UniProt
VAR_033380
R
33
Q
2B11_HUMAN
Polymorphism
34716432
B/E
R
4
Q
04
UniProt
VAR_016740
Q
39
E
2B11_HUMAN
Polymorphism
---
B/E
Q
10
E
05
UniProt
VAR_033381
S
66
Y
2B11_HUMAN
Polymorphism
16822820
B/E
S
37
Y
06
UniProt
VAR_016741
G
74
R
2B11_HUMAN
Polymorphism
---
B/E
G
45
R
07
UniProt
VAR_033382
Y
76
F
2B11_HUMAN
Polymorphism
1060346
B/E
Y
47
F
08
UniProt
VAR_033383
Y
89
S
2B11_HUMAN
Polymorphism
36074728
B/E
Y
60
S
09
UniProt
VAR_016710
L
96
I
2B11_HUMAN
Polymorphism
---
B/E
L
67
I
10
UniProt
VAR_016711
Q
99
D
2B11_HUMAN
Polymorphism
---
B/E
Q
70
D
11
UniProt
VAR_033384
Q
99
E
2B11_HUMAN
Polymorphism
17881965
B/E
Q
70
E
12
UniProt
VAR_033385
Q
99
H
2B11_HUMAN
Polymorphism
17879599
B/E
Q
70
H
13
UniProt
VAR_016742
R
100
A
2B11_HUMAN
Polymorphism
---
B/E
R
71
A
14
UniProt
VAR_016712
R
100
E
2B11_HUMAN
Polymorphism
---
B/E
R
71
E
15
UniProt
VAR_033386
A
102
G
2B11_HUMAN
Polymorphism
17878857
B/E
A
73
G
16
UniProt
VAR_033387
A
103
E
2B11_HUMAN
Polymorphism
16822805
B/E
A
74
E
17
UniProt
VAR_016713
T
106
N
2B11_HUMAN
Polymorphism
16822752
B/E
T
77
N
18
UniProt
VAR_033388
Y
107
H
2B11_HUMAN
Polymorphism
16822512
B/E
Y
78
H
19
UniProt
VAR_016714
V
114
A
2B11_HUMAN
Polymorphism
17424145
B/E
V
85
A
20
UniProt
VAR_016715
G
115
V
2B11_HUMAN
Polymorphism
2230810
B/E
G
86
V
21
UniProt
VAR_033389
G
164
D
2B11_HUMAN
Polymorphism
1059633
B/E
G
135
D
22
UniProt
VAR_033390
A
169
T
2B11_HUMAN
Polymorphism
2308768
B/E
A
140
T
23
UniProt
VAR_033391
V
171
M
2B11_HUMAN
Polymorphism
701829
B/E
V
142
M
24
UniProt
VAR_033392
Q
178
H
2B11_HUMAN
Polymorphism
701830
B/E
Q
149
H
25
UniProt
VAR_023459
K
191
E
CD4_HUMAN
Polymorphism
28917504
G/H
K
166
E
26
UniProt
VAR_033393
R
195
Q
2B11_HUMAN
Polymorphism
3205588
B/E
R
166
Q
27
UniProt
VAR_033394
T
210
I
2B11_HUMAN
Polymorphism
17423930
B/E
T
181
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:161-167,D:161-167,B:171-177,E:17...)
;
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.
DRA_HUMAN
186-192
2
A:161-167
D:161-167
2B11_HUMAN
200-206
2
B:171-177
E:171-177
[
close PROSITE info
]
Exons
(12, 24)
Info
All Exons
Exon 1.3 (G:2-47 | H:0-47)
Exon 1.4 (G:47-100 | H:47-100)
Exon 1.5 (G:100-178 (gaps) | H:100-178 (gaps...)
Exon 1.6b (G:178-178 | H:178-178)
Exon 2.3 (B:0-5 | E:0-5)
Exon 2.4 (B:5-95 | E:5-95)
Exon 2.5b (B:95-189 | E:95-189)
Exon 2.6 (B:189-190 | E:189-190)
Exon 3.6a (A:3-3 | D:3-3)
Exon 3.7b (A:3-85 | D:3-85)
Exon 3.8c (A:85-179 | D:85-179)
Exon 3.9a (A:179-180 | D:179-181)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6b
05: Boundary 1.6b/1.7
06: Boundary -/2.3
07: Boundary 2.3/2.4
08: Boundary 2.4/2.5b
09: Boundary 2.5b/2.6
10: Boundary 2.6/2.7
11: Boundary -/3.6a
12: Boundary 3.6a/3.7b
13: Boundary 3.7b/3.8c
14: Boundary 3.8c/3.9a
15: Boundary 3.9a/3.10b
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
1.1
ENST00000011653
1
ENSE00001303311
chr12:
6898651-6898828
178
CD4_HUMAN
-
0
0
-
-
1.2
ENST00000011653
2
ENSE00000866954
chr12:
6909238-6909353
116
CD4_HUMAN
1-17
17
0
-
-
1.3
ENST00000011653
3
ENSE00000716042
chr12:
6909473-6909637
165
CD4_HUMAN
17-72
56
2
G:2-47
H:0-47
46
48
1.4
ENST00000011653
4
ENSE00000716044
chr12:
6923308-6923466
159
CD4_HUMAN
72-125
54
2
G:47-100
H:47-100
54
54
1.5
ENST00000011653
5
ENSE00000716046
chr12:
6923925-6924158
234
CD4_HUMAN
125-203
79
2
G:100-178 (gaps)
H:100-178 (gaps)
79
79
1.6b
ENST00000011653
6b
ENSE00000716048
chr12:
6925222-6925569
348
CD4_HUMAN
203-319
117
2
G:178-178
H:178-178
1
1
1.7
ENST00000011653
7
ENSE00000716051
chr12:
6926296-6926496
201
CD4_HUMAN
319-386
68
0
-
-
1.8
ENST00000011653
8
ENSE00000716053
chr12:
6927587-6927708
122
CD4_HUMAN
386-426
41
0
-
-
1.9
ENST00000011653
9
ENSE00000716057
chr12:
6928013-6928080
68
CD4_HUMAN
427-449
23
0
-
-
1.10
ENST00000011653
10
ENSE00001182623
chr12:
6928465-6929976
1512
CD4_HUMAN
449-458
10
0
-
-
2.3
ENST00000360004
3
ENSE00001930619
chr6:
32557625-32557420
206
2B11_HUMAN
1-34
34
2
B:0-5
E:0-5
6
6
2.4
ENST00000360004
4
ENSE00001731226
chr6:
32552155-32551886
270
2B11_HUMAN
34-124
91
2
B:5-95
E:5-95
91
91
2.5b
ENST00000360004
5b
ENSE00001801024
chr6:
32549615-32549334
282
2B11_HUMAN
124-218
95
2
B:95-189
E:95-189
95
95
2.6
ENST00000360004
6
ENSE00001717727
chr6:
32548633-32548523
111
2B11_HUMAN
218-255
38
2
B:189-190
E:189-190
2
2
2.7
ENST00000360004
7
ENSE00001773376
chr6:
32548047-32548024
24
2B11_HUMAN
255-263
9
0
-
-
2.8
ENST00000360004
8
ENSE00001954617
chr6:
32546881-32546546
336
2B11_HUMAN
263-266
4
0
-
-
3.6a
ENST00000383259
6a
ENSE00001839042
HSCHR6_MHC_QBL:32365090-32365280
191
DRA_HUMAN
1-28
28
2
A:3-3
D:3-3
1
1
3.7b
ENST00000383259
7b
ENSE00001719010
HSCHR6_MHC_QBL:32367694-32367939
246
DRA_HUMAN
28-110
83
2
A:3-85
D:3-85
83
83
3.8c
ENST00000383259
8c
ENSE00001737588
HSCHR6_MHC_QBL:32368431-32368712
282
DRA_HUMAN
110-204
95
2
A:85-179
D:85-179
95
95
3.9a
ENST00000383259
9a
ENSE00001770912
HSCHR6_MHC_QBL:32369002-32369167
166
DRA_HUMAN
204-254
51
2
A:179-180
D:179-181
2
3
3.10b
ENST00000383259
10b
ENSE00001925700
HSCHR6_MHC_QBL:32369906-32370300
395
DRA_HUMAN
-
0
0
-
-
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SCOP Domains
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (193 KB)
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