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.
1V4T
Asym. Unit
Info
Asym.Unit (74 KB)
Biol.Unit 1 (69 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 GLUCOKINASE
Authors
:
K. Kamata, M. Mitsuya, T. Nishimura, J. Eiki, Y. Nagata
Date
:
19 Nov 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hexokinase Iv, Allosteric Enzyme, Diabetes, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Kamata, M. Mitsuya, T. Nishimura, J. Eiki, Y. Nagata
Structural Basis For Allosteric Regulation Of The Monomeric Allosteric Enzyme Human Glucokinase
Structure V. 12 429 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: SODIUM ION (NAa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
1
Ligand/Ion
SODIUM ION
2
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:227 , THR A:228 , GLY A:410 , SER A:411 , NA A:602
BINDING SITE FOR RESIDUE SO4 A 600
2
AC2
SOFTWARE
HIS A:424 , ARG A:428 , HOH A:604
BINDING SITE FOR RESIDUE SO4 A 601
3
AC3
SOFTWARE
ASP A:409 , SO4 A:600
BINDING SITE FOR RESIDUE NA A 602
[
close Site info
]
SAPs(SNPs)/Variants
(42, 42)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_010584 (R36W, chain A, )
02: VAR_010585 (A53S, chain A, )
03: VAR_003693 (E70K, chain A, )
04: VAR_003694 (G80A, chain A, )
05: VAR_003695 (G80S, chain A, )
06: VAR_003696 (M107T, chain A, )
07: VAR_010586 (Y108H, chain A, )
08: VAR_012352 (I110T, chain A, )
09: VAR_012353 (A119D, chain A, )
10: VAR_003697 (S131P, chain A, )
11: VAR_010587 (H137R, chain A, )
12: VAR_010588 (F150S, chain A, )
13: VAR_003699 (V182M, chain A, )
14: VAR_003700 (A188T, chain A, )
15: VAR_003701 (V203A, chain A, )
16: VAR_010590 (T209M, chain A, )
17: VAR_012351 (M210K, chain A, )
18: VAR_010591 (M210T, chain A, )
19: VAR_010592 (C213R, chain A, )
20: VAR_003702 (E221K, chain A, )
21: VAR_003703 (V226M, chain A, )
22: VAR_003704 (G227C, chain A, )
23: VAR_003705 (T228M, chain A, )
24: VAR_003706 (E256K, chain A, )
25: VAR_003707 (W257R, chain A, )
26: VAR_010593 (A259T, chain A, )
27: VAR_010594 (G261E, chain A, )
28: VAR_003708 (G261R, chain A, )
29: VAR_003709 (E279Q, chain A, )
30: VAR_003710 (G299R, chain A, )
31: VAR_003712 (E300K, chain A, )
32: VAR_003711 (E300Q, chain A, )
33: VAR_003713 (L309P, chain A, )
34: VAR_010595 (S336L, chain A, )
35: VAR_066615 (T342P, chain A, )
36: VAR_010596 (V367M, chain A, )
37: VAR_010597 (C382Y, chain A, )
38: VAR_010598 (A384T, chain A, )
39: VAR_012354 (G385V, chain A, )
40: VAR_010599 (R392C, chain A, )
41: VAR_003714 (K414E, chain A, )
42: VAR_003715 (V455M, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_010584
R
36
W
HXK4_HUMAN
Disease (MODY2)
---
A
R
36
W
02
UniProt
VAR_010585
A
53
S
HXK4_HUMAN
Disease (MODY2)
---
A
A
53
S
03
UniProt
VAR_003693
E
70
K
HXK4_HUMAN
Disease (MODY2)
---
A
E
70
K
04
UniProt
VAR_003694
G
80
A
HXK4_HUMAN
Disease (MODY2)
---
A
G
80
A
05
UniProt
VAR_003695
G
80
S
HXK4_HUMAN
Disease (MODY2)
---
A
G
80
S
06
UniProt
VAR_003696
M
107
T
HXK4_HUMAN
Polymorphism
---
A
M
107
T
07
UniProt
VAR_010586
Y
108
H
HXK4_HUMAN
Disease (MODY2)
---
A
Y
108
H
08
UniProt
VAR_012352
I
110
T
HXK4_HUMAN
Disease (MODY2)
---
A
I
110
T
09
UniProt
VAR_012353
A
119
D
HXK4_HUMAN
Disease (MODY2)
---
A
A
119
D
10
UniProt
VAR_003697
S
131
P
HXK4_HUMAN
Disease (MODY2)
---
A
S
131
P
11
UniProt
VAR_010587
H
137
R
HXK4_HUMAN
Disease (MODY2)
---
A
H
137
R
12
UniProt
VAR_010588
F
150
S
HXK4_HUMAN
Disease (MODY2)
---
A
F
150
S
13
UniProt
VAR_003699
V
182
M
HXK4_HUMAN
Disease (MODY2)
---
A
V
182
M
14
UniProt
VAR_003700
A
188
T
HXK4_HUMAN
Disease (MODY2)
---
A
A
188
T
15
UniProt
VAR_003701
V
203
A
HXK4_HUMAN
Disease (MODY2)
---
A
V
203
A
16
UniProt
VAR_010590
T
209
M
HXK4_HUMAN
Disease (MODY2)
---
A
T
209
M
17
UniProt
VAR_012351
M
210
K
HXK4_HUMAN
Disease (MODY2)
---
A
M
210
K
18
UniProt
VAR_010591
M
210
T
HXK4_HUMAN
Disease (MODY2)
---
A
M
210
T
19
UniProt
VAR_010592
C
213
R
HXK4_HUMAN
Disease (MODY2)
---
A
C
213
R
20
UniProt
VAR_003702
E
221
K
HXK4_HUMAN
Disease (MODY2)
---
A
E
221
K
21
UniProt
VAR_003703
V
226
M
HXK4_HUMAN
Disease (MODY2)
---
A
V
226
M
22
UniProt
VAR_003704
G
227
C
HXK4_HUMAN
Disease (MODY2)
---
A
G
227
C
23
UniProt
VAR_003705
T
228
M
HXK4_HUMAN
Disease (MODY2)
---
A
T
228
M
24
UniProt
VAR_003706
E
256
K
HXK4_HUMAN
Disease (MODY2)
---
A
E
256
K
25
UniProt
VAR_003707
W
257
R
HXK4_HUMAN
Disease (MODY2)
---
A
W
257
R
26
UniProt
VAR_010593
A
259
T
HXK4_HUMAN
Disease (MODY2)
---
A
A
259
T
27
UniProt
VAR_010594
G
261
E
HXK4_HUMAN
Disease (MODY2)
---
A
G
261
E
28
UniProt
VAR_003708
G
261
R
HXK4_HUMAN
Disease (MODY2)
---
A
G
261
R
29
UniProt
VAR_003709
E
279
Q
HXK4_HUMAN
Disease (MODY2)
104894005
A
E
279
Q
30
UniProt
VAR_003710
G
299
R
HXK4_HUMAN
Disease (MODY2)
---
A
G
299
R
31
UniProt
VAR_003712
E
300
K
HXK4_HUMAN
Disease (MODY2)
---
A
E
300
K
32
UniProt
VAR_003711
E
300
Q
HXK4_HUMAN
Disease (MODY2)
---
A
E
300
Q
33
UniProt
VAR_003713
L
309
P
HXK4_HUMAN
Disease (MODY2)
---
A
L
309
P
34
UniProt
VAR_010595
S
336
L
HXK4_HUMAN
Disease (MODY2)
---
A
S
336
L
35
UniProt
VAR_066615
T
342
P
HXK4_HUMAN
Polymorphism
---
A
T
342
P
36
UniProt
VAR_010596
V
367
M
HXK4_HUMAN
Disease (MODY2)
---
A
V
367
M
37
UniProt
VAR_010597
C
382
Y
HXK4_HUMAN
Disease (MODY2)
---
A
C
382
Y
38
UniProt
VAR_010598
A
384
T
HXK4_HUMAN
Disease (MODY2)
---
A
A
384
T
39
UniProt
VAR_012354
G
385
V
HXK4_HUMAN
Disease (MODY2)
---
A
G
385
V
40
UniProt
VAR_010599
R
392
C
HXK4_HUMAN
Disease (MODY2)
---
A
R
392
C
41
UniProt
VAR_003714
K
414
E
HXK4_HUMAN
Disease (MODY2)
---
A
K
414
E
42
UniProt
VAR_003715
V
455
M
HXK4_HUMAN
Disease (HHF3)
---
A
V
455
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: HEXOKINASE_1 (A:146-156)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEXOKINASE_1
PS00378
Hexokinase domain signature.
HXK4_HUMAN
146-171
1
A:146-156
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1v4ta1 (A:15-218)
1b: SCOP_d1v4ta2 (A:219-461)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Hexokinase
(19)
Protein domain
:
Glucokinase
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1v4ta1
A:15-218
1b
d1v4ta2
A:219-461
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1v4tA01 (A:15-59,A:218-444)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Hexokinase; domain 1
(22)
Homologous Superfamily
:
[code=3.40.367.20, no name defined]
(22)
Human (Homo sapiens)
(16)
1a
1v4tA01
A:15-59,A:218-444
[
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
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 (74 KB)
Header - Asym.Unit
Biol.Unit 1 (69 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
1V4T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
