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.
PLEASE WAIT...
Getting 'Exon' information from database.
2W41
Asym. Unit
Info
Asym.Unit (179 KB)
Biol.Unit 1 (172 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 PLASMODIUM FALCIPARUM GLYCEROL KINASE WITH ADP
Authors
:
C. Schnick, S. D. Polley, Q. L. Fivelman, L. Ranford-Cartwright, S. R. Wilkinson, J. A. Brannigan, A. J. Wilkinson, D. A. Baker
Date
:
18 Nov 08 (Deposition) - 02 Dec 08 (Release) - 03 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.41
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Closed Conformation, Kinase, Malaria, Plasmodium, Transferase, Sugar Kinase/Hsp70/Actin Superfamily, Glycerol Kinase, Open Conformation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Schnick, S. D. Polley, Q. L. Fivelman, L. Ranford-Cartwright, S. R. Wilkinson, J. A. Brannigan, A. J. Wilkinson, D. A. Baker
Structure And Non-Essential Function Of Glycerol Kinase In Plasmodium Falciparum Blood Stages.
Mol. Microbiol. V. 71 533 2009
[
close entry info
]
Hetero Components
(2, 23)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
EDO
21
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY B:267 , THR B:268 , GLY B:313 , VAL B:316 , PRO B:328 , ALA B:331 , SER B:332 , GLY B:413 , GLY B:414 , MET B:415 , ASN B:418
BINDING SITE FOR RESIDUE ADP B1502
02
AC2
SOFTWARE
GLY A:267 , THR A:268 , GLY A:313 , VAL A:316 , PRO A:328 , ALA A:331 , SER A:332 , GLY A:413 , GLY A:414 , MET A:415 , ASN A:418 , HOH A:2145 , HOH A:2146 , HOH A:2147
BINDING SITE FOR RESIDUE ADP A1502
03
AC3
SOFTWARE
ILE A:309 , THR A:311 , ALA A:312 , PHE A:350 , SER A:351 , GLY A:352 , HOH A:2088 , HOH A:2148 , PHE B:371
BINDING SITE FOR RESIDUE EDO A1503
04
AC4
SOFTWARE
SER B:10 , THR B:11 , GLN B:12
BINDING SITE FOR RESIDUE EDO B1503
05
AC5
SOFTWARE
PHE A:371 , ILE B:309 , THR B:311 , ALA B:312 , PHE B:350 , SER B:351 , GLY B:352 , HOH B:2152 , HOH B:2153
BINDING SITE FOR RESIDUE EDO B1504
06
AC6
SOFTWARE
VAL B:72 , ILE B:73 , ILE B:74 , ASP B:234
BINDING SITE FOR RESIDUE EDO B1505
07
AC7
SOFTWARE
TYR B:293 , LYS B:294 , PHE B:295 , ASP B:299 , LYS B:300 , LYS B:302
BINDING SITE FOR RESIDUE EDO B1506
08
AC8
SOFTWARE
ARG A:83 , GLU A:84 , ASP A:246 , EDO A:1508
BINDING SITE FOR RESIDUE EDO A1504
09
AC9
SOFTWARE
ASP A:123 , LYS A:127
BINDING SITE FOR RESIDUE EDO A1505
10
BC1
SOFTWARE
ILE A:62 , LYS A:66 , VAL A:72 , ILE A:73 , ILE A:74
BINDING SITE FOR RESIDUE EDO A1506
11
BC2
SOFTWARE
VAL A:182 , LEU A:196 , ILE A:217 , LYS A:218 , LYS A:294 , ASP A:297 , HOH A:2056
BINDING SITE FOR RESIDUE EDO A1507
12
BC3
SOFTWARE
TYR B:367 , ARG B:496 , HOH B:2145
BINDING SITE FOR RESIDUE EDO B1507
13
BC4
SOFTWARE
GLU A:84 , EDO A:1504 , EDO A:1509
BINDING SITE FOR RESIDUE EDO A1508
14
BC5
SOFTWARE
GLU B:84 , TYR B:135 , EDO B:1509 , EDO B:1513 , HOH B:2154
BINDING SITE FOR RESIDUE EDO B1508
15
BC6
SOFTWARE
GLN B:82 , ARG B:83 , GLU B:84 , ASP B:246 , EDO B:1508
BINDING SITE FOR RESIDUE EDO B1509
16
BC7
SOFTWARE
GLU B:259 , GLY B:277 , GLU B:278 , HOH B:2083
BINDING SITE FOR RESIDUE EDO B1510
17
BC8
SOFTWARE
PHE B:388 , ASN B:391 , GLU B:392 , THR B:487 , TRP B:490 , ASN B:491 , HOH B:2155
BINDING SITE FOR RESIDUE EDO B1511
18
BC9
SOFTWARE
TYR A:135 , EDO A:1508
BINDING SITE FOR RESIDUE EDO A1509
19
CC1
SOFTWARE
GLN A:197 , TRP A:198 , ILE A:217
BINDING SITE FOR RESIDUE EDO A1510
20
CC2
SOFTWARE
ASP A:479 , LYS A:481 , ASP B:479 , ASP B:480 , LYS B:481
BINDING SITE FOR RESIDUE EDO A1511
21
CC3
SOFTWARE
GLN B:197 , TRP B:198 , GLU B:216 , ILE B:217
BINDING SITE FOR RESIDUE EDO B1512
22
CC4
SOFTWARE
SER A:10 , THR A:11 , ASP A:246 , HOH A:2152
BINDING SITE FOR RESIDUE EDO A1512
23
CC5
SOFTWARE
EDO B:1508
BINDING SITE FOR RESIDUE EDO B1513
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(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, 4)
Info
All SCOP Domains
1a: SCOP_d2w41a1 (A:-4-254)
1b: SCOP_d2w41b1 (B:-5-254)
1c: SCOP_d2w41b2 (B:255-501)
1d: SCOP_d2w41a2 (A:255-501)
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)
Plasmodium falciparum [TaxId: 36329]
(2)
1a
d2w41a1
A:-4-254
1b
d2w41b1
B:-5-254
1c
d2w41b2
B:255-501
1d
d2w41a2
A:255-501
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_FGGY_C_2w41B01 (B:262-454)
1b: PFAM_FGGY_C_2w41B02 (B:262-454)
2a: PFAM_FGGY_N_2w41B03 (B:3-253)
2b: PFAM_FGGY_N_2w41B04 (B:3-253)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Actin_ATPase
(173)
Family
:
FGGY_C
(10)
Plasmodium falciparum (isolate 3D7)
(2)
1a
FGGY_C-2w41B01
B:262-454
1b
FGGY_C-2w41B02
B:262-454
Family
:
FGGY_N
(10)
Plasmodium falciparum (isolate 3D7)
(2)
2a
FGGY_N-2w41B03
B:3-253
2b
FGGY_N-2w41B04
B:3-253
[
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
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 (179 KB)
Header - Asym.Unit
Biol.Unit 1 (172 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
2W41
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
