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.
2XCV
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (335 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 THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND 2,3-BISPHOSPHOGLYCERATE
Authors
:
K. Wallden, P. Nordlund
Date
:
26 Apr 10 (Deposition) - 16 Mar 11 (Release) - 20 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Hydrolase, Metal-Binding, Nucleotide Metabolism
(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
]
Hetero Components
(4, 4)
Info
All Hetero Components
1a: (2R)-2,3-DIPHOSPHOGLYCERIC ACID (DG2a)
2a: GLYCEROL (GOLa)
3a: INOSINIC ACID (IMPa)
4a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DG2
1
Ligand/Ion
(2R)-2,3-DIPHOSPHOGLYCERIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
IMP
1
Ligand/Ion
INOSINIC ACID
4
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:144 , LYS A:362 , ARG A:456 , TYR A:457
BINDING SITE FOR RESIDUE DG2 A1489
2
AC2
SOFTWARE
PHE A:283 , ASP A:284 , LEU A:285 , ILE A:286 , GLN A:322 , GLY A:324 , ILE A:325 , HOH A:2256
BINDING SITE FOR RESIDUE GOL A1490
3
AC3
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:1492 , HOH A:2107 , HOH A:2215 , HOH A:2218 , HOH A:2257
BINDING SITE FOR RESIDUE IMP A1491
4
AC4
SOFTWARE
ASN A:52 , ASP A:54 , ASP A:351 , IMP A:1491 , HOH A:2215 , HOH A:2218
BINDING SITE FOR RESIDUE MG A1492
[
close Site info
]
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)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
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:387-396)
Exon 1.24 (A:421-424)
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:387-396
10
1.24
ENST00000343289
24
ENSE00001610324
chr10:
104850753-104850693
61
5NTC_HUMAN
404-424
21
1
A:421-424
4
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
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_5_nucleotid_2xcvA01 (A:35-488)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
5_nucleotid
(10)
Homo sapiens (Human)
(10)
1a
5_nucleotid-2xcvA01
A:35-488
[
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
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 (92 KB)
Header - Asym.Unit
Biol.Unit 1 (335 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
2XCV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
