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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
3G25
Biol. Unit 2
Info
Asym.Unit (373 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (360 KB)
Biol.Unit 3 (183 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.9 ANGSTROM CRYSTAL STRUCTURE OF GLYCEROL KINASE (GLPK) FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH GLYCEROL.
Authors
:
G. Minasov, T. Skarina, O. Onopriyenko, A. Savchenko, W. F. Anderson, C Structural Genomics Of Infectious Diseases (Csgid)
Date
:
30 Jan 09 (Deposition) - 17 Feb 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Glycerol Kinase, Glycerol, Idp00743, Atp-Binding, Glycerol Metabolism, Kinase, Nucleotide-Binding, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Minasov, T. Skarina, O. Onopriyenko, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 9 Angstrom Crystal Structure Of Glycerol Kinase (Glpk) From Staphylococcus Aureus In Complex With Glycerol.
To Be Published
[
close entry info
]
Hetero Components
(3, 61)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
4f: PHOSPHATE ION (PO4f)
4g: PHOSPHATE ION (PO4g)
4h: PHOSPHATE ION (PO4h)
4i: PHOSPHATE ION (PO4i)
4j: PHOSPHATE ION (PO4j)
4k: PHOSPHATE ION (PO4k)
4l: PHOSPHATE ION (PO4l)
4m: PHOSPHATE ION (PO4m)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
MSE
44
Mod. Amino Acid
SELENOMETHIONINE
3
NA
-1
Ligand/Ion
SODIUM ION
4
PO4
13
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:82 , GLU A:83 , TRP A:102 , TYR A:134 , ASP A:244 , GLN A:245 , PHE A:269 , NA A:500 , PO4 A:502
BINDING SITE FOR RESIDUE GOL A 499
02
AC2
SOFTWARE
THR A:266 , GLY A:267 , PHE A:269 , GOL A:499 , PO4 A:502
BINDING SITE FOR RESIDUE NA A 500
03
AC3
SOFTWARE
GLN A:22 , PHE A:452 , PO4 A:505
BINDING SITE FOR RESIDUE NA A 501
04
AC4
SOFTWARE
GLY A:11 , THR A:12 , ASP A:244 , GLY A:265 , THR A:266 , GOL A:499 , NA A:500 , HOH A:592 , HOH A:599 , HOH A:671
BINDING SITE FOR RESIDUE PO4 A 502
05
AC5
SOFTWARE
TYR A:331 , LYS A:372 , HOH A:669 , ARG B:320 , NA B:501
BINDING SITE FOR RESIDUE PO4 A 503
06
AC6
SOFTWARE
SER A:337 , THR A:338 , ARG A:377 , GLU A:381 , PHE A:420 , LEU A:481 , HOH A:579 , HOH A:595
BINDING SITE FOR RESIDUE PO4 A 504
07
AC7
SOFTWARE
GLN A:22 , TRP A:453 , GLU A:454 , SER A:455 , ASP A:458 , NA A:501 , LYS C:23
BINDING SITE FOR RESIDUE PO4 A 505
08
AC8
SOFTWARE
LYS A:171 , GLY A:174 , TYR A:229 , HIS A:230
BINDING SITE FOR RESIDUE PO4 A 506
09
AC9
SOFTWARE
ARG B:82 , GLU B:83 , TRP B:102 , TYR B:134 , ASP B:244 , GLN B:245 , PHE B:269 , PO4 B:503 , HOH B:663
BINDING SITE FOR RESIDUE GOL B 499
10
BC1
SOFTWARE
THR B:12 , THR B:13 , PO4 B:503
BINDING SITE FOR RESIDUE NA B 500
11
BC2
SOFTWARE
PO4 A:503
BINDING SITE FOR RESIDUE NA B 501
12
BC3
SOFTWARE
LYS B:171 , LYS B:175 , PO4 B:504
BINDING SITE FOR RESIDUE NA B 502
13
BC4
SOFTWARE
GLY B:11 , THR B:12 , GLY B:265 , THR B:266 , GOL B:499 , NA B:500 , HOH B:575 , HOH B:620 , HOH B:663
BINDING SITE FOR RESIDUE PO4 B 503
14
BC5
SOFTWARE
LYS B:171 , GLY B:174 , LYS B:175 , TYR B:229 , HIS B:230 , NA B:502
BINDING SITE FOR RESIDUE PO4 B 504
15
BC6
SOFTWARE
SER B:337 , THR B:338 , ARG B:377 , GLU B:381 , PHE B:420 , LEU B:481 , HOH B:671 , HOH B:957
BINDING SITE FOR RESIDUE PO4 B 505
16
BC7
SOFTWARE
ARG A:320 , TYR B:331 , LYS B:372 , HOH B:632 , HOH B:876 , HOH B:1115
BINDING SITE FOR RESIDUE PO4 B 506
17
BC8
SOFTWARE
GLN C:81 , ARG C:82 , GLU C:83 , TRP C:102 , TYR C:134 , ASP C:244 , GLN C:245 , PHE C:269 , PO4 C:500
BINDING SITE FOR RESIDUE GOL C 499
18
BC9
SOFTWARE
THR C:12 , THR C:13 , GLY C:265 , THR C:266 , GOL C:499 , HOH C:598 , HOH C:1083
BINDING SITE FOR RESIDUE PO4 C 500
19
CC1
SOFTWARE
GLN D:81 , ARG D:82 , GLU D:83 , TRP D:102 , TYR D:134 , ASP D:244 , GLN D:245 , PHE D:269 , PO4 D:502
BINDING SITE FOR RESIDUE GOL D 499
20
CC2
SOFTWARE
THR D:12 , THR D:13 , SER D:14 , ARG D:16 , PO4 D:502
BINDING SITE FOR RESIDUE NA D 500
21
CC3
SOFTWARE
LYS C:372 , ARG D:320 , PO4 D:504
BINDING SITE FOR RESIDUE NA D 501
22
CC4
SOFTWARE
THR D:12 , GLY D:265 , THR D:266 , GOL D:499 , NA D:500 , HOH D:842 , HOH D:1108
BINDING SITE FOR RESIDUE PO4 D 502
23
CC5
SOFTWARE
ARG C:320 , TYR D:331 , LYS D:372 , HOH D:965
BINDING SITE FOR RESIDUE PO4 D 503
24
CC6
SOFTWARE
TYR C:331 , LYS C:372 , ARG D:320 , NA D:501
BINDING SITE FOR RESIDUE PO4 D 504
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FGGY_KINASES_2 (A:361-381,B:361-381,C:361-381,D:36...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FGGY_KINASES_2
PS00445
FGGY family of carbohydrate kinases signature 2.
GLPK_STAAC
361-381
4
A:361-381
B:361-381
C:361-381
D:361-381
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3g25a1 (A:0-252)
1b: SCOP_d3g25a2 (A:253-498)
1c: SCOP_d3g25b1 (B:0-252)
1d: SCOP_d3g25b2 (B:253-498)
1e: SCOP_d3g25c1 (C:1-252)
1f: SCOP_d3g25c2 (C:253-498)
1g: SCOP_d3g25d1 (D:0-252)
1h: SCOP_d3g25d2 (D:253-498)
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
:
automated matches
(111)
Protein domain
:
automated matches
(111)
Staphylococcus aureus [TaxId: 93062]
(2)
1a
d3g25a1
A:0-252
1b
d3g25a2
A:253-498
1c
d3g25b1
B:0-252
1d
d3g25b2
B:253-498
1e
d3g25c1
C:1-252
1f
d3g25c2
C:253-498
1g
d3g25d1
D:0-252
1h
d3g25d2
D:253-498
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3g25A02 (A:253-498)
1b: CATH_3g25A01 (A:0-252)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Aureus col (Staphylococcus aureus subsp)
(1)
1a
3g25A02
A:253-498
1b
3g25A01
A:0-252
[
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
Chain D
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 (373 KB)
Header - Asym.Unit
Biol.Unit 1 (185 KB)
Header - Biol.Unit 1
Biol.Unit 2 (360 KB)
Header - Biol.Unit 2
Biol.Unit 3 (183 KB)
Header - Biol.Unit 3
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
3G25
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
