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.
4KXW
Asym. Unit
Info
Asym.Unit (267 KB)
Biol.Unit 1 (519 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-XYLULOSE-5-PHOSPHATE, CRYSTAL 2
Authors
:
P. Neumann, S. Luedtke, R. Ficner, K. Tittmann
Date
:
28 May 13 (Deposition) - 21 Aug 13 (Release) - 04 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
0.97
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Thiamin Diphosphate, Enzyme Catalysis, Pentose Phosphate Pathway, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Ludtke, P. Neumann, K. M. Erixon, F. Leeper, R. Kluger, R. Ficner, K. Tittmann
Sub-Angstrom-Resolution Crystallography Reveals Physical Distortions That Enhance Reactivity Of A Covalent Enzymatic Intermediate.
Nat Chem V. 5 762 2013
[
close entry info
]
Hetero Components
(5, 17)
Info
All Hetero Components
1a: D-XYLITOL-5-PHOSPHATE (DX5a)
1b: D-XYLITOL-5-PHOSPHATE (DX5b)
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)
3a: MAGNESIUM ION (MGa)
4a: SODIUM ION (NAa)
5a: THIAMIN DIPHOSPHATE (TDPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DX5
2
Ligand/Ion
D-XYLITOL-5-PHOSPHATE
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
NA
1
Ligand/Ion
SODIUM ION
5
TDP
1
Ligand/Ion
THIAMIN DIPHOSPHATE
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:155 , ASN A:185 , LEU A:187 , TDP A:1015 , HOH A:7001
BINDING SITE FOR RESIDUE MG A 1001
02
AC2
SOFTWARE
PRO A:63 , ASN A:68 , ASP A:69 , ARG A:70 , PHE A:71 , ARG A:379 , HOH A:7186 , HOH A:7847
BINDING SITE FOR RESIDUE EDO A 1002
03
AC3
SOFTWARE
TYR A:564 , ALA A:588 , ASN A:590 , HOH A:7051 , HOH A:7055 , HOH A:7126 , HOH A:7247
BINDING SITE FOR RESIDUE EDO A 1003
04
AC4
SOFTWARE
PHE A:71 , VAL A:72 , LEU A:73 , LEU A:82 , PHE A:117 , HOH A:7040 , HOH A:7056 , HOH A:7068
BINDING SITE FOR RESIDUE EDO A 1004
05
AC5
SOFTWARE
ASP A:155 , GLY A:156 , LEU A:158 , SER A:159 , TRP A:164 , PRO A:194 , LEU A:195 , TYR A:202 , ARG A:205 , EDO A:1012 , HOH A:7467 , HOH A:7960 , HOH A:7961
BINDING SITE FOR RESIDUE EDO A 1005
06
AC6
SOFTWARE
LEU A:92 , LEU A:107 , GLN A:115 , HOH A:7110 , HOH A:7124 , HOH A:7174 , HOH A:7920
BINDING SITE FOR RESIDUE EDO A 1006
07
AC7
SOFTWARE
GLN A:10 , ASN A:590 , ARG A:591 , HOH A:7260
BINDING SITE FOR RESIDUE EDO A 1007
08
AC8
SOFTWARE
TYR A:137 , TYR A:141 , TYR A:173 , HOH A:7409 , HOH A:7610 , HOH A:7914
BINDING SITE FOR RESIDUE EDO A 1008
09
AC9
SOFTWARE
ALA A:33 , ARG A:101 , GLU A:423 , LYS A:597 , HOH A:7103 , HOH A:7586 , HOH A:7742 , HOH A:7934
BINDING SITE FOR RESIDUE EDO A 1009
10
BC1
SOFTWARE
ARG A:21 , SER A:25 , ALA A:84 , GLU A:88 , GLU A:94 , LEU A:97 , LYS A:283 , HOH A:7177 , HOH A:7472 , HOH A:7672
BINDING SITE FOR RESIDUE EDO A 1010
11
BC2
SOFTWARE
PHE A:142 , ASP A:333 , ARG A:358 , HOH A:7406 , HOH A:7539 , HOH A:7700 , HOH A:7894
BINDING SITE FOR RESIDUE EDO A 1011
12
BC3
SOFTWARE
LEU A:158 , SER A:159 , TRP A:164 , GLU A:165 , ALA A:168 , PHE A:209 , EDO A:1005 , EDO A:1014 , HOH A:7961
BINDING SITE FOR RESIDUE EDO A 1012
13
BC4
SOFTWARE
ASN A:411 , ALA A:461 , THR A:464 , CYS A:468 , HOH A:7070 , HOH A:7081
BINDING SITE FOR RESIDUE NA A 1013
14
BC5
SOFTWARE
SER A:159 , GLU A:165 , ALA A:168 , EDO A:1012 , HOH A:7467 , HOH A:7715
BINDING SITE FOR RESIDUE EDO A 1014
15
BC6
SOFTWARE
SER A:40 , LYS A:75 , HIS A:77 , GLY A:123 , SER A:124 , LEU A:125 , GLY A:154 , ASP A:155 , GLY A:156 , GLU A:157 , GLU A:160 , ASN A:185 , LEU A:187 , GLY A:188 , GLN A:189 , LYS A:244 , HIS A:258 , ASP A:341 , ILE A:364 , GLU A:366 , PHE A:392 , ARG A:395 , GLN A:428 , MG A:1001 , DX5 A:1016 , HOH A:7001
BINDING SITE FOR RESIDUE TDP A 1015
16
BC7
SOFTWARE
HIS A:37 , HIS A:77 , HIS A:110 , GLN A:189 , HIS A:258 , SER A:345 , PHE A:389 , HIS A:416 , ASP A:424 , GLN A:428 , ARG A:474 , TDP A:1015 , DX5 A:1017 , HOH A:7053 , HOH A:7095 , HOH A:7108 , HOH A:7246 , HOH A:7263 , HOH A:7299
BINDING SITE FOR RESIDUE DX5 A 1016
17
BC8
SOFTWARE
HIS A:37 , GLN A:189 , HIS A:258 , ARG A:318 , SER A:345 , HIS A:416 , ASP A:424 , ARG A:474 , DX5 A:1016 , HOH A:7108 , HOH A:7246 , HOH A:7263 , HOH A:7272 , HOH A:7299
BINDING SITE FOR RESIDUE DX5 A 1017
[
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
(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
(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 (267 KB)
Header - Asym.Unit
Biol.Unit 1 (519 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
4KXW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help