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3IAR
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (130 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF HUMAN ADENOSINE DEAMINASE
Authors
:
E. Ugochukwu, Y. Zhang, E. Hapka, W. W. Yue, J. E. Bray, J. Muniz, N. Burge A. Chaikuad, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A K. L. Kavanagh, U. Oppermann, Structural Genomics Consortium (Sg
Date
:
14 Jul 09 (Deposition) - 11 Aug 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.52
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Deaminase, Adenosine Deaminase, Adenosine, Purine Metabolism, Structural Genomics, Structural Genomics Consortium, Sgc, Disease Mutation, Hereditary Hemolytic Anemia, Hydrolase, Nucleotide Metabolism, Scid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Ugochukwu, Y. Zhang, E. Hapka, W. W. Yue, J. E. Bray, J. Muniz, N. Burgess-Brown, A. Chaikuad, K. L. Kavanagh, U. Oppermann
The Crystal Structure Of Human Adenosine Deaminase
To Be Published
[
close entry info
]
Hetero Components
(4, 5)
Info
All Hetero Components
1a: (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-Y... (3D1a)
2a: GLYCEROL (GOLa)
3a: NICKEL (II) ION (NIa)
4a: NITRATE ION (NO3a)
4b: NITRATE ION (NO3b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3D1
1
Ligand/Ion
(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL
2
GOL
1
Ligand/Ion
GLYCEROL
3
NI
1
Ligand/Ion
NICKEL (II) ION
4
NO3
2
Ligand/Ion
NITRATE ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
NI A:1 , HIS A:17 , ASP A:19 , LEU A:62 , PHE A:65 , LEU A:106 , GLY A:184 , HIS A:214 , GLU A:217 , HIS A:238 , ASP A:295 , ASP A:296 , HOH A:781 , HOH A:814
BINDING SITE FOR RESIDUE 3D1 A 501
2
AC2
SOFTWARE
HIS A:15 , HIS A:17 , HIS A:214 , ASP A:295 , 3D1 A:501
BINDING SITE FOR RESIDUE NI A 1
3
AC3
SOFTWARE
LYS A:111 , THR A:125 , PRO A:126 , ASP A:127 , LYS A:164 , HOH A:727 , HOH A:1058
BINDING SITE FOR RESIDUE NO3 A 371
4
AC4
SOFTWARE
PRO A:5 , PHE A:7 , ASP A:8 , LYS A:11 , TYR A:29 , ARG A:33 , GLU A:93 , ASP A:305 , HOH A:702 , HOH A:827
BINDING SITE FOR RESIDUE NO3 A 2
5
AC5
SOFTWARE
PRO A:116 , TRP A:117 , HIS A:157 , HOH A:397 , HOH A:485 , HOH A:613 , HOH A:795 , HOH A:797
BINDING SITE FOR RESIDUE GOL A 372
[
close Site info
]
SAPs(SNPs)/Variants
(32, 32)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_002209 (D8N, chain A, )
02: VAR_002210 (H15D, chain A, )
03: VAR_002211 (G20R, chain A, )
04: VAR_002212 (G74C, chain A, )
05: VAR_002213 (R76W, chain A, )
06: VAR_002214 (K80R, chain A, )
07: VAR_002215 (A83D, chain A, )
08: VAR_002216 (R101L, chain A, )
09: VAR_002218 (R101Q, chain A, )
10: VAR_002217 (R101W, chain A, )
11: VAR_002219 (L107P, chain A, )
12: VAR_002220 (V129M, chain A, )
13: VAR_002221 (G140E, chain A, )
14: VAR_002222 (R142Q, chain A, )
15: VAR_002223 (R149Q, chain A, )
16: VAR_002224 (R149W, chain A, )
17: VAR_002225 (L152M, chain A, )
18: VAR_002226 (R156C, chain A, )
19: VAR_002227 (R156H, chain A, )
20: VAR_002228 (V177M, chain A, )
21: VAR_002229 (A179D, chain A, )
22: VAR_002230 (Q199P, chain A, )
23: VAR_002231 (R211C, chain A, )
24: VAR_002232 (R211H, chain A, )
25: VAR_002233 (A215T, chain A, )
26: VAR_002234 (G216R, chain A, )
27: VAR_002235 (T233I, chain A, )
28: VAR_002236 (P274L, chain A, )
29: VAR_002237 (S291L, chain A, )
30: VAR_002238 (P297Q, chain A, )
31: VAR_002239 (L304R, chain A, )
32: VAR_002240 (A329V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_002209
D
8
N
ADA_HUMAN
Polymorphism
73598374
A
D
8
N
02
UniProt
VAR_002210
H
15
D
ADA_HUMAN
Disease (ADASCID)
121908725
A
H
15
D
03
UniProt
VAR_002211
G
20
R
ADA_HUMAN
Disease (ADASCID)
121908724
A
G
20
R
04
UniProt
VAR_002212
G
74
C
ADA_HUMAN
Disease (ADASCID)
121908730
A
G
74
C
05
UniProt
VAR_002213
R
76
W
ADA_HUMAN
Disease (ADASCID)
121908736
A
R
76
W
06
UniProt
VAR_002214
K
80
R
ADA_HUMAN
Polymorphism
11555566
A
K
80
R
07
UniProt
VAR_002215
A
83
D
ADA_HUMAN
Disease (ADASCID)
121908726
A
A
83
D
08
UniProt
VAR_002216
R
101
L
ADA_HUMAN
Disease (ADASCID)
121908720
A
R
101
L
09
UniProt
VAR_002218
R
101
Q
ADA_HUMAN
Disease (ADASCID)
28930970
A
R
101
Q
10
UniProt
VAR_002217
R
101
W
ADA_HUMAN
Disease (ADASCID)
28930969
A
R
101
W
11
UniProt
VAR_002219
L
107
P
ADA_HUMAN
Disease (ADASCID)
121908739
A
L
107
P
12
UniProt
VAR_002220
V
129
M
ADA_HUMAN
Disease (ADASCID)
121908731
A
V
129
M
13
UniProt
VAR_002221
G
140
E
ADA_HUMAN
Disease (ADASCID)
121908732
A
G
140
E
14
UniProt
VAR_002222
R
142
Q
ADA_HUMAN
Unclassified
61732239
A
R
142
Q
15
UniProt
VAR_002223
R
149
Q
ADA_HUMAN
Disease (ADASCID)
121908737
A
R
149
Q
16
UniProt
VAR_002224
R
149
W
ADA_HUMAN
Disease (ADASCID)
121908733
A
R
149
W
17
UniProt
VAR_002225
L
152
M
ADA_HUMAN
Polymorphism
121908728
A
L
152
M
18
UniProt
VAR_002226
R
156
C
ADA_HUMAN
Disease (ADASCID)
121908735
A
R
156
C
19
UniProt
VAR_002227
R
156
H
ADA_HUMAN
Disease (ADASCID)
121908722
A
R
156
H
20
UniProt
VAR_002228
V
177
M
ADA_HUMAN
Disease (ADASCID)
121908719
A
V
177
M
21
UniProt
VAR_002229
A
179
D
ADA_HUMAN
Disease (ADASCID)
121908727
A
A
179
D
22
UniProt
VAR_002230
Q
199
P
ADA_HUMAN
Disease (ADASCID)
121908734
A
Q
199
P
23
UniProt
VAR_002231
R
211
C
ADA_HUMAN
Disease (ADASCID)
121908740
A
R
211
C
24
UniProt
VAR_002232
R
211
H
ADA_HUMAN
Disease (ADASCID)
121908716
A
R
211
H
25
UniProt
VAR_002233
A
215
T
ADA_HUMAN
Disease (ADASCID)
114025668
A
A
215
T
26
UniProt
VAR_002234
G
216
R
ADA_HUMAN
Disease (ADASCID)
121908723
A
G
216
R
27
UniProt
VAR_002235
T
233
I
ADA_HUMAN
Polymorphism
121908729
A
T
233
I
28
UniProt
VAR_002236
P
274
L
ADA_HUMAN
Disease (ADASCID)
121908738
A
P
274
L
29
UniProt
VAR_002237
S
291
L
ADA_HUMAN
Disease (ADASCID)
121908721
A
S
291
L
30
UniProt
VAR_002238
P
297
Q
ADA_HUMAN
Disease (ADASCID)
121908718
A
P
297
Q
31
UniProt
VAR_002239
L
304
R
ADA_HUMAN
Disease (ADASCID)
---
A
L
304
R
32
UniProt
VAR_002240
A
329
V
ADA_HUMAN
Disease (ADASCID)
121908715
A
A
329
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: A_DEAMINASE (A:291-297)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
A_DEAMINASE
PS00485
Adenosine and AMP deaminase signature.
ADA_HUMAN
291-297
1
A:291-297
[
close PROSITE info
]
Exons
(12, 12)
Info
All Exons
Exon 1.1a (A:5-11)
Exon 1.2 (A:12-32)
Exon 1.3 (A:32-73)
Exon 1.4a (A:73-121)
Exon 1.5 (A:121-160)
Exon 1.6 (A:160-202)
Exon 1.7a (A:203-226)
Exon 1.7c (A:227-260)
Exon 1.8 (A:261-282)
Exon 1.9a (A:282-325)
Exon 1.9c (A:326-360)
Exon 1.10b (A:360-363)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4a
05: Boundary 1.4a/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7a
08: Boundary 1.7a/1.7c
09: Boundary 1.7c/1.8
10: Boundary 1.8/1.9a
11: Boundary 1.9a/1.9c
12: Boundary 1.9c/1.10b
13: Boundary 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
1.1a
ENST00000372874
1a
ENSE00001458877
chr20:
43280383-43280216
168
ADA_HUMAN
1-11
11
1
A:5-11
7
1.2
ENST00000372874
2
ENSE00001377681
chr20:
43264929-43264868
62
ADA_HUMAN
12-32
21
1
A:12-32
21
1.3
ENST00000372874
3
ENSE00000662275
chr20:
43257810-43257688
123
ADA_HUMAN
32-73
42
1
A:32-73
42
1.4a
ENST00000372874
4a
ENSE00000662274
chr20:
43255240-43255097
144
ADA_HUMAN
73-121
49
1
A:73-121
49
1.5
ENST00000372874
5
ENSE00000662273
chr20:
43254325-43254210
116
ADA_HUMAN
121-160
40
1
A:121-160
40
1.6
ENST00000372874
6
ENSE00000662272
chr20:
43252970-43252843
128
ADA_HUMAN
160-202
43
1
A:160-202
43
1.7a
ENST00000372874
7a
ENSE00000662271
chr20:
43251719-43251648
72
ADA_HUMAN
203-226
24
1
A:203-226
24
1.7c
ENST00000372874
7c
ENSE00001273220
chr20:
43251571-43251470
102
ADA_HUMAN
227-260
34
1
A:227-260
34
1.8
ENST00000372874
8
ENSE00001273210
chr20:
43251293-43251229
65
ADA_HUMAN
261-282
22
1
A:261-282
22
1.9a
ENST00000372874
9a
ENSE00001273283
chr20:
43249788-43249659
130
ADA_HUMAN
282-325
44
1
A:282-325
44
1.9c
ENST00000372874
9c
ENSE00000844877
chr20:
43249042-43248940
103
ADA_HUMAN
326-360
35
1
A:326-360
35
1.10b
ENST00000372874
10b
ENSE00001954810
chr20:
43248488-43248163
326
ADA_HUMAN
360-363
4
1
A:360-363
4
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3iara_ (A:)
View:
Select:
Label:
Classes
(
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(
)
Folds
(
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(
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Superfamilies
(
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(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Adenosine/AMP deaminase
(36)
Protein domain
:
Adenosine deaminase (ADA)
(24)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d3iara_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3iarA00 (A:5-364)
View:
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Classes
(
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Topologies
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Human (Homo sapiens)
(5)
1a
3iarA00
A:5-364
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
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Atom Selection
(currently selected atoms:
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