PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1HYR
Asym. Unit
Info
Asym.Unit (87 KB)
Biol.Unit 1 (82 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MICA IN COMPLEX WITH NATURAL KILLER CELL RECEPTOR NKG2D
Authors
:
P. Li, R. K. Strong
Date
:
21 Jan 01 (Deposition) - 23 May 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Activating Nk Cell Receptor, Nkg2D, C-Type-Lectin Like, Mic- A, Mhc-I, Complex, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Li, D. L. Morris, B. E. Willcox, A. Steinle, T. Spies, R. K. Strong
Complex Structure Of The Activating Immunoreceptor Nkg2D And Its Mhc Class I-Like Ligand Mica.
Nat. Immunol. V. 2 443 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(31, 32)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_043625 (R6P, chain C, )
02: VAR_043626 (W14G, chain C, )
03: VAR_043627 (T24A, chain C, )
04: VAR_043628 (V26G, chain C, )
05: VAR_043629 (C36Y, chain C, )
06: VAR_043630 (Q91R, chain C, )
07: VAR_043631 (R105K, chain C, )
08: VAR_043632 (G114R, chain C, )
09: VAR_043633 (L122V, chain C, )
10: VAR_043634 (T124S, chain C, )
11: VAR_043635 (K125E, chain C, )
12: VAR_043636 (M129V, chain C, )
13: VAR_043637 (V142I, chain C, )
14: VAR_043638 (M151V, chain C, )
15: VAR_043639 (H156L, chain C, )
16: VAR_043640 (K173E, chain C, )
17: VAR_043641 (G175S, chain C, )
18: VAR_043642 (V176I, chain C, )
19: VAR_030738 (N177S, chain A/B, )
20: VAR_043643 (T181R, chain C, )
21: VAR_043644 (G206S, chain C, )
22: VAR_043645 (Y208C, chain C, )
23: VAR_043646 (W210R, chain C, )
24: VAR_043647 (T213I, chain C, )
25: VAR_043648 (S215T, chain C, )
26: VAR_043649 (V221L, chain C, )
27: VAR_043869 (W230S, chain C, )
28: VAR_043650 (Q251R, chain C, )
29: VAR_043651 (R256S, chain C, )
30: VAR_043652 (S268G, chain C, )
31: VAR_043653 (P271A, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_043625
R
29
P
MICA_HUMAN
Polymorphism
9380254
C
R
6
P
02
UniProt
VAR_043626
W
37
G
MICA_HUMAN
Polymorphism
1063630
C
W
14
G
03
UniProt
VAR_043627
T
47
A
MICA_HUMAN
Polymorphism
1051785
C
T
24
A
04
UniProt
VAR_043628
V
49
G
MICA_HUMAN
Polymorphism
17200158
C
V
26
G
05
UniProt
VAR_043629
C
59
Y
MICA_HUMAN
Polymorphism
1051786
C
C
36
Y
06
UniProt
VAR_043630
Q
114
R
MICA_HUMAN
Polymorphism
41558312
C
Q
91
R
07
UniProt
VAR_043631
R
128
K
MICA_HUMAN
Polymorphism
41557113
C
R
105
K
08
UniProt
VAR_043632
G
137
R
MICA_HUMAN
Polymorphism
41556715
C
G
114
R
09
UniProt
VAR_043633
L
145
V
MICA_HUMAN
Polymorphism
1051790
C
L
122
V
10
UniProt
VAR_043634
T
147
S
MICA_HUMAN
Polymorphism
41539919
C
T
124
S
11
UniProt
VAR_043635
K
148
E
MICA_HUMAN
Polymorphism
1051791
C
K
125
E
12
UniProt
VAR_043636
M
152
V
MICA_HUMAN
Polymorphism
1051792
C
M
129
V
13
UniProt
VAR_043637
V
165
I
MICA_HUMAN
Polymorphism
3819269
C
V
142
I
14
UniProt
VAR_043638
M
174
V
MICA_HUMAN
Polymorphism
41560824
C
M
151
V
15
UniProt
VAR_043639
H
179
L
MICA_HUMAN
Polymorphism
3819268
C
H
156
L
16
UniProt
VAR_043640
K
196
E
MICA_HUMAN
Polymorphism
1051794
C
K
173
E
17
UniProt
VAR_043641
G
198
S
MICA_HUMAN
Polymorphism
1131896
C
G
175
S
18
UniProt
VAR_043642
V
199
I
MICA_HUMAN
Polymorphism
41549718
C
V
176
I
19
UniProt
VAR_030738
N
177
S
NKG2D_HUMAN
Polymorphism
2306182
A/B
N
177
S
20
UniProt
VAR_043643
T
204
R
MICA_HUMAN
Polymorphism
1131897
C
T
181
R
21
UniProt
VAR_043644
G
229
S
MICA_HUMAN
Polymorphism
1131898
C
G
206
S
22
UniProt
VAR_043645
Y
231
C
MICA_HUMAN
Polymorphism
41546915
C
Y
208
C
23
UniProt
VAR_043646
W
233
R
MICA_HUMAN
Polymorphism
1051798
C
W
210
R
24
UniProt
VAR_043647
T
236
I
MICA_HUMAN
Polymorphism
1140700
C
T
213
I
25
UniProt
VAR_043648
S
238
T
MICA_HUMAN
Polymorphism
1051799
C
S
215
T
26
UniProt
VAR_043649
V
244
L
MICA_HUMAN
Polymorphism
41540613
C
V
221
L
27
UniProt
VAR_043869
W
253
S
MICA_HUMAN
Polymorphism
---
C
W
230
S
28
UniProt
VAR_043650
Q
274
R
MICA_HUMAN
Polymorphism
1063635
C
Q
251
R
29
UniProt
VAR_043651
R
279
S
MICA_HUMAN
Polymorphism
41557614
C
R
256
S
30
UniProt
VAR_043652
S
291
G
MICA_HUMAN
Polymorphism
---
C
S
268
G
31
UniProt
VAR_043653
P
294
A
MICA_HUMAN
Polymorphism
41553616
C
P
271
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_2 (A:106-212,B:106-212)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C_TYPE_LECTIN_2
PS50041
C-type lectin domain profile.
NKG2D_HUMAN
106-212
2
A:106-212
B:106-212
[
close PROSITE info
]
Exons
(8, 12)
Info
All Exons
Exon 1.5 (A:93-93 | B:89-93)
Exon 1.6a (A:93-143 | B:93-143)
Exon 1.7 (A:144-178 | B:144-178)
Exon 1.8 (A:178-216 | B:178-216)
Exon 2.3a (C:0-1)
Exon 2.4 (C:1-86)
Exon 2.5b (C:86-182)
Exon 2.6 (C:182-274)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4/1.5
02: Boundary 1.5/1.6a
03: Boundary 1.6a/1.7
04: Boundary 1.7/1.8
05: Boundary 1.8/-
06: Boundary 2.2/2.3a
07: Boundary 2.3a/2.4
08: Boundary 2.4/2.5b
09: Boundary 2.5b/2.6
10: Boundary 2.6/2.7
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
ENST00000240618
1
ENSE00001524992
chr12:
10542640-10542542
99
NKG2D_HUMAN
-
0
0
-
-
1.2
ENST00000240618
2
ENSE00002198225
chr12:
10541474-10541370
105
NKG2D_HUMAN
1-14
14
0
-
-
1.3
ENST00000240618
3
ENSE00001656271
chr12:
10539609-10539502
108
NKG2D_HUMAN
14-50
37
0
-
-
1.4
ENST00000240618
4
ENSE00001160615
chr12:
10532391-10532299
93
NKG2D_HUMAN
50-81
32
0
-
-
1.5
ENST00000240618
5
ENSE00001160608
chr12:
10532081-10532046
36
NKG2D_HUMAN
81-93
13
2
A:93-93
B:89-93
1
5
1.6a
ENST00000240618
6a
ENSE00001160601
chr12:
10531304-10531153
152
NKG2D_HUMAN
93-143
51
2
A:93-143
B:93-143
51
51
1.7
ENST00000240618
7
ENSE00000821886
chr12:
10530834-10530731
104
NKG2D_HUMAN
144-178
35
2
A:144-178
B:144-178
35
35
1.8
ENST00000240618
8
ENSE00001160593
chr12:
10525830-10524953
878
NKG2D_HUMAN
178-216
39
2
A:178-216
B:178-216
39
39
2.1c
ENST00000400325
1c
ENSE00001802778
HSCHR6_MHC_QBL:31358575-31358589
15
MICA_HUMAN
-
0
0
-
-
2.2
ENST00000400325
2
ENSE00001765771
HSCHR6_MHC_QBL:31359983-31360182
200
MICA_HUMAN
-
0
0
-
-
2.3a
ENST00000400325
3a
ENSE00001778375
HSCHR6_MHC_QBL:31361271-31361528
258
MICA_HUMAN
1-24
24
1
C:0-1
2
2.4
ENST00000400325
4
ENSE00001751066
HSCHR6_MHC_QBL:31368470-31368724
255
MICA_HUMAN
24-109
86
1
C:1-86
86
2.5b
ENST00000400325
5b
ENSE00001651377
HSCHR6_MHC_QBL:31368999-31369286
288
MICA_HUMAN
109-205
97
1
C:86-182
97
2.6
ENST00000400325
6
ENSE00001666138
HSCHR6_MHC_QBL:31369874-31370152
279
MICA_HUMAN
205-298
94
1
C:182-274
93
2.7
ENST00000400325
7
ENSE00001497291
HSCHR6_MHC_QBL:31370253-31370384
132
MICA_HUMAN
298-342
45
0
-
-
2.8a
ENST00000400325
8a
ENSE00001672548
HSCHR6_MHC_QBL:31372936-31373183
248
MICA_HUMAN
342-383
42
0
-
-
[
close EXON info
]
SCOP Domains
(3, 4)
Info
All SCOP Domains
1a: SCOP_d1hyrc1 (C:181-274)
2a: SCOP_d1hyra_ (A:)
2b: SCOP_d1hyrb_ (B:)
3a: SCOP_d1hyrc2 (C:0-180)
View:
Select:
Label:
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 I MHC homolog, alpha-3 domain
(6)
Human (Homo sapiens), Mic-a [TaxId: 9606]
(2)
1a
d1hyrc1
C:181-274
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
C-type lectin domain
(182)
Protein domain
:
NK cell-activating receptor nkg2d
(5)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d1hyra_
A:
2b
d1hyrb_
B:
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC homolog
(6)
Human (Homo sapiens), Mic-a [TaxId: 9606]
(2)
3a
d1hyrc2
C:0-180
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1hyrC01 (C:1-180)
2a: CATH_1hyrB00 (B:89-216)
2b: CATH_1hyrA00 (A:93-216)
3a: CATH_1hyrC02 (C:181-273)
View:
Select:
Label:
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
1hyrC01
C:1-180
Architecture
:
Roll
(3276)
Topology
:
Mannose-Binding Protein A; Chain A
(180)
Homologous Superfamily
:
Mannose-Binding Protein A, subunit A
(180)
Human (Homo sapiens)
(80)
2a
1hyrB00
B:89-216
2b
1hyrA00
A:93-216
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
3a
1hyrC02
C:181-273
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (87 KB)
Header - Asym.Unit
Biol.Unit 1 (82 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1HYR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help