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.
4KQX
Asym. Unit
Info
Asym.Unit (120 KB)
Biol.Unit 1 (112 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MUTANT SLACKIA EXIGUA KARI DDV IN COMPLEX WITH NAD AND AN INHIBITOR
Authors
:
S. Brinkmann-Chen, T. Flock, J. K. B. Cahn, C. D. Snow, E. M. Brustad, J. A. Mcintosh, P. Meinhold, L. Zhang, F. H. Arnold
Date
:
15 May 13 (Deposition) - 26 Jun 13 (Release) - 17 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cofactor Switch, Rossmann Fold, Ketol-Acid Reductoisomerase, Acetohydroxyacid Isomeroreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Brinkmann-Chen, T. Flock, J. K. Cahn, C. D. Snow, E. M. Brustad, J. A. Mcintosh, P. Meinhold, L. Zhang, F. H. Arnold
General Approach To Reversing Ketol-Acid Reductoisomerase Cofactor Dependence From Nadph To Nadh.
Proc. Natl. Acad. Sci. Usa V. 110 10946 2013
[
close entry info
]
Hetero Components
(4, 15)
Info
All Hetero Components
1a: N-HYDROXY-N-ISOPROPYLOXAMIC ACID (HIOa)
1b: N-HYDROXY-N-ISOPROPYLOXAMIC ACID (HIOb)
2a: HISTIDINE (HISa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HIO
2
Ligand/Ion
N-HYDROXY-N-ISOPROPYLOXAMIC ACID
2
HIS
1
Mod. Amino Acid
HISTIDINE
3
MG
10
Ligand/Ion
MAGNESIUM ION
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:34 , TYR A:35 , GLY A:36 , SER A:37 , GLN A:38 , ARG A:58 , ASP A:61 , LEU A:90 , VAL A:91 , PRO A:92 , ASP A:93 , VAL A:95 , GLN A:96 , VAL A:99 , ALA A:117 , HIS A:118 , PRO A:140 , PRO A:143 , GLY A:144 , HOH A:515 , HOH A:527 , HOH A:541 , HOH A:559 , HOH A:565 , HOH A:610 , HOH A:616 , SER B:260 , ILE B:261 , SER B:262 , HIO B:401 , MG B:406 , HOH B:633 , HOH B:639
BINDING SITE FOR RESIDUE NAD A 401
02
AC2
SOFTWARE
GLU A:241 , ILE A:261 , SER A:262 , ALA A:265 , PRO B:143 , ASP B:201 , GLU B:205 , CYS B:210 , NAD B:402 , MG B:407 , MG B:409 , HOH B:514 , HOH B:516 , HOH B:632
BINDING SITE FOR RESIDUE HIO A 402
03
AC3
SOFTWARE
ASN A:258 , ILE A:261 , SER A:262 , ASN A:263 , GLU A:266
BINDING SITE FOR RESIDUE MG A 403
04
AC4
SOFTWARE
TYR A:259 , SER A:260 , ILE A:261 , HOH A:595 , NAD B:402
BINDING SITE FOR RESIDUE MG A 404
05
AC5
SOFTWARE
ASP A:201 , MG A:406 , HOH A:602 , HIO B:401 , HOH B:628 , HOH B:634
BINDING SITE FOR RESIDUE MG A 405
06
AC6
SOFTWARE
ASP A:201 , GLU A:205 , MG A:405 , HOH A:605 , HIO B:401 , HOH B:633
BINDING SITE FOR RESIDUE MG A 406
07
AC7
SOFTWARE
PRO A:143 , ASP A:201 , GLU A:205 , CYS A:210 , NAD A:401 , MG A:405 , MG A:406 , HOH A:602 , HOH A:605 , GLU B:241 , ILE B:261 , SER B:262 , ALA B:265 , HOH B:628 , HOH B:633 , HOH B:634
BINDING SITE FOR RESIDUE HIO B 401
08
AC8
SOFTWARE
SER A:260 , ILE A:261 , SER A:262 , HIO A:402 , MG A:404 , TYR B:35 , GLY B:36 , SER B:37 , GLN B:38 , ARG B:58 , ASP B:61 , LEU B:90 , VAL B:91 , PRO B:92 , ASP B:93 , GLN B:96 , VAL B:99 , ALA B:117 , HIS B:118 , PRO B:140 , GLY B:142 , PRO B:143 , GLY B:144 , MG B:408 , HOH B:508 , HOH B:514 , HOH B:516 , HOH B:557 , HOH B:560 , HOH B:583 , HOH B:641
BINDING SITE FOR RESIDUE NAD B 402
09
AC9
SOFTWARE
GLN A:280 , ALA A:284 , HOH A:560 , HOH A:561 , HOH A:601 , ASN B:278 , GLU B:341 , ASP B:342 , LEU B:343 , GLU B:344 , HOH B:548 , HOH B:597 , HOH B:646
BINDING SITE FOR RESIDUE HIS B 403
10
BC1
SOFTWARE
ASN B:258 , ILE B:261 , SER B:262 , ASN B:263 , GLU B:266
BINDING SITE FOR RESIDUE MG B 404
11
BC2
SOFTWARE
ALA B:81 , GLU B:82 , ALA B:84 , HIS B:107 , ASN B:112 , HOH B:649
BINDING SITE FOR RESIDUE MG B 405
12
BC3
SOFTWARE
SER A:37 , NAD A:401 , TYR B:259 , SER B:260 , ILE B:261 , HOH B:639
BINDING SITE FOR RESIDUE MG B 406
13
BC4
SOFTWARE
HIO A:402 , HOH A:502 , HOH A:504 , ASP B:201 , HOH B:516
BINDING SITE FOR RESIDUE MG B 407
14
BC5
SOFTWARE
GLY B:36 , SER B:37 , GLN B:38 , GLY B:39 , LEU B:90 , NAD B:402
BINDING SITE FOR RESIDUE MG B 408
15
BC6
SOFTWARE
HIO A:402 , ASP B:201 , GLU B:205 , HOH B:514 , HOH B:632
BINDING SITE FOR RESIDUE MG B 409
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4kqxa2 (A:194-335)
1b: SCOP_d4kqxb2 (B:194-344)
2a: SCOP_d4kqxa1 (A:14-193)
2b: SCOP_d4kqxb1 (B:10-193)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Slackia exigua [TaxId: 649764]
(2)
1a
d4kqxa2
A:194-335
1b
d4kqxb2
B:194-344
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Slackia exigua [TaxId: 649764]
(2)
2a
d4kqxa1
A:14-193
2b
d4kqxb1
B:10-193
[
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
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 (120 KB)
Header - Asym.Unit
Biol.Unit 1 (112 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
4KQX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help