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Asym. Unit
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Asym.Unit (182 KB)
Biol.Unit 1 (683 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND ATP
Authors
:
K. Wallden, P. Nordlund
Date
:
26 Apr 10 (Deposition) - 16 Mar 11 (Release) - 27 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Cn-Ii, Gmp-Imp Specific Nucleotidase, High Km 5-Prime Nucleotidase, Hydrolase, Metal-Binding, Nt5C2, Nucleotide Metabolism, Nucleotide- Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Wallden, P. Nordlund
Structural Basis For The Allosteric Regulation And Substrate Recognition Of Human Cytosolic 5'-Nucleotidase Ii
J. Mol. Biol. V. 408 684 2011
[
close entry info
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: INOSINIC ACID (IMPa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
GOL
6
Ligand/Ion
GLYCEROL
3
IMP
1
Ligand/Ion
INOSINIC ACID
4
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
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:144 , ASP A:145 , THR A:147 , ILE A:152 , ASN A:154 , PHE A:354 , LYS A:362 , GLN A:453 , ARG A:456 , TYR A:457 , GOL A:1495 , MG A:1497 , HOH A:2154 , HOH A:2386 , HOH A:2387 , HOH A:2388 , HOH A:2389 , HOH A:2390 , HOH A:2391 , HOH A:2392 , HOH A:2393 , HOH A:2394 , HOH A:2395 , HOH A:2396 , HOH A:2397
BINDING SITE FOR RESIDUE ATP A1489
02
AC2
SOFTWARE
ASN A:52 , MET A:53 , ASP A:54 , PHE A:157 , ARG A:202 , ASP A:206 , HIS A:209 , TYR A:210 , LYS A:215 , THR A:249 , ASN A:250 , SER A:251 , LYS A:292 , MG A:1498 , HOH A:2170 , HOH A:2214 , HOH A:2283 , HOH A:2331 , HOH A:2332 , HOH A:2398 , HOH A:2399 , HOH A:2400
BINDING SITE FOR RESIDUE IMP A1490
03
AC3
SOFTWARE
PHE A:283 , ASP A:284 , LEU A:321 , GLN A:322 , HIS A:323 , GLY A:324 , ILE A:325 , HOH A:2274 , HOH A:2401
BINDING SITE FOR RESIDUE GOL A1491
04
AC4
SOFTWARE
PHE A:198 , GLN A:199 , ARG A:202 , ASP A:206 , HOH A:2402 , HOH A:2403
BINDING SITE FOR RESIDUE GOL A1492
05
AC5
SOFTWARE
PRO A:96 , THR A:97 , GLU A:374 , GLU A:378 , TYR A:434 , HOH A:2344 , HOH A:2404 , HOH A:2405
BINDING SITE FOR RESIDUE GOL A1493
06
AC6
SOFTWARE
ASP A:257 , THR A:261 , PRO A:278 , TRP A:279 , GLN A:280 , HOH A:2240 , HOH A:2406
BINDING SITE FOR RESIDUE GOL A1494
07
AC7
SOFTWARE
TYR A:151 , ILE A:152 , LEU A:153 , ASN A:154 , ASN A:158 , HIS A:352 , ATP A:1489 , HOH A:2407 , HOH A:2409
BINDING SITE FOR RESIDUE GOL A1495
08
AC8
SOFTWARE
ASP A:252 , TYR A:253 , VAL A:288 , ASP A:289 , GLY A:310 , LEU A:312
BINDING SITE FOR RESIDUE GOL A1496
09
AC9
SOFTWARE
ATP A:1489 , HOH A:2396
BINDING SITE FOR RESIDUE MG A1497
10
BC1
SOFTWARE
ASN A:52 , ASP A:54 , ASP A:351 , IMP A:1490 , HOH A:2331 , HOH A:2332
BINDING SITE FOR RESIDUE MG A1498
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024244 (T3A, chain A, )
2: VAR_030242 (Q136R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024244
T
3
A
5NTC_HUMAN
Polymorphism
10883841
A
T
3
A
2
UniProt
VAR_030242
Q
136
R
5NTC_HUMAN
Polymorphism
12262171
A
Q
136
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(17, 17)
Info
All Exons
Exon 1.3 (A:3-34)
Exon 1.6 (A:34-59)
Exon 1.8a (A:59-98)
Exon 1.9a (A:98-130)
Exon 1.11 (A:130-161)
Exon 1.12 (A:161-180)
Exon 1.15 (A:180-211)
Exon 1.16a (A:212-229)
Exon 1.18b (A:230-257)
Exon 1.19 (A:258-271)
Exon 1.20b (A:272-307)
Exon 1.21a (A:308-330)
Exon 1.22 (A:330-387)
Exon 1.23 (A:387-400)
Exon 1.24 (A:417-424)
Exon 1.25 (A:425-483)
Exon 1.26d (A:484-488)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.3
02: Boundary 1.3/1.6
03: Boundary 1.6/1.8a
04: Boundary 1.8a/1.9a
05: Boundary 1.9a/1.11
06: Boundary 1.11/1.12
07: Boundary 1.12/1.15
08: Boundary 1.15/1.16a
09: Boundary 1.16a/1.18b
10: Boundary 1.18b/1.19
11: Boundary 1.19/1.20b
12: Boundary 1.20b/1.21a
13: Boundary 1.21a/1.22
14: Boundary 1.22/1.23
15: Boundary 1.23/1.24
16: Boundary 1.24/1.25
17: Boundary 1.25/1.26d
18: Boundary 1.26d/-
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
ENST00000343289
1a
ENSE00001759705
chr10:
104953056-104952993
64
5NTC_HUMAN
-
0
0
-
-
1.3
ENST00000343289
3
ENSE00002186305
chr10:
104934739-104934615
125
5NTC_HUMAN
1-34
34
1
A:3-34
32
1.6
ENST00000343289
6
ENSE00001787725
chr10:
104899236-104899163
74
5NTC_HUMAN
34-59
26
1
A:34-59
26
1.8a
ENST00000343289
8a
ENSE00001707803
chr10:
104866463-104866346
118
5NTC_HUMAN
59-98
40
1
A:59-98
40
1.9a
ENST00000343289
9a
ENSE00001645482
chr10:
104865558-104865463
96
5NTC_HUMAN
98-130
33
1
A:98-130
33
1.11
ENST00000343289
11
ENSE00001742963
chr10:
104861083-104860992
92
5NTC_HUMAN
130-161
32
1
A:130-161
32
1.12
ENST00000343289
12
ENSE00001739246
chr10:
104860859-104860802
58
5NTC_HUMAN
161-180
20
1
A:161-180
20
1.15
ENST00000343289
15
ENSE00001753876
chr10:
104859776-104859683
94
5NTC_HUMAN
180-211
32
1
A:180-211
32
1.16a
ENST00000343289
16a
ENSE00001705007
chr10:
104858741-104858688
54
5NTC_HUMAN
212-229
18
1
A:212-229
18
1.18b
ENST00000343289
18b
ENSE00002152144
chr10:
104857131-104857048
84
5NTC_HUMAN
230-257
28
1
A:230-257
28
1.19
ENST00000343289
19
ENSE00001748493
chr10:
104855737-104855696
42
5NTC_HUMAN
258-271
14
1
A:258-271
14
1.20b
ENST00000343289
20b
ENSE00001646238
chr10:
104854212-104854105
108
5NTC_HUMAN
272-307
36
1
A:272-307
36
1.21a
ENST00000343289
21a
ENSE00001596497
chr10:
104853795-104853729
67
5NTC_HUMAN
308-330
23
1
A:308-330
23
1.22
ENST00000343289
22
ENSE00001711453
chr10:
104853066-104852896
171
5NTC_HUMAN
330-387
58
1
A:330-387
58
1.23
ENST00000343289
23
ENSE00001659728
chr10:
104851372-104851321
52
5NTC_HUMAN
387-404
18
1
A:387-400
14
1.24
ENST00000343289
24
ENSE00001610324
chr10:
104850753-104850693
61
5NTC_HUMAN
404-424
21
1
A:417-424
8
1.25
ENST00000343289
25
ENSE00001778811
chr10:
104850544-104850368
177
5NTC_HUMAN
425-483
59
1
A:425-483
59
1.26d
ENST00000343289
26d
ENSE00001648268
chr10:
104849665-104845940
3726
5NTC_HUMAN
484-561
78
1
A:484-488
5
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_5_nucleotid_2xcwA01 (A:35-488)
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(
)
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)
Clan
:
HAD
(186)
Family
:
5_nucleotid
(10)
Homo sapiens (Human)
(10)
1a
5_nucleotid-2xcwA01
A:35-488
[
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Chain A
Asymmetric Unit 1
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