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.
4HCH
Biol. Unit 1
Info
Asym.Unit (151 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (564 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 D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM AND L-TARTRATE
Authors
:
A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Date
:
29 Sep 12 (Deposition) - 24 Oct 12 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (4x)
Keywords
:
Enolase Fold, D-Glucarate Dehydratase, D-Glucarate, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium And L-Tartrate
To Be Published
[
close entry info
]
Hetero Components
(4, 7)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: TRIETHYLENE GLYCOL (PGEa)
6a: L(+)-TARTARIC ACID (TLAa)
6b: L(+)-TARTARIC ACID (TLAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
3
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
6
TLA
1
Ligand/Ion
L(+)-TARTARIC ACID
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:24 , CYS A:139 , HIS A:171 , HIS A:209 , HIS A:309 , GOL A:402 , HOH A:527 , HOH A:555 , HOH A:585 , HOH A:708 , HOH A:950 , ARG B:90
BINDING SITE FOR RESIDUE TLA A 401
02
AC2
SOFTWARE
HIS A:309 , GLY A:310 , ASN A:311 , GLU A:329 , GLY A:331 , LEU A:332 , TLA A:401 , HOH A:586 , HOH A:733 , HOH A:951
BINDING SITE FOR RESIDUE GOL A 402
03
AC3
SOFTWARE
PRO A:181 , TYR A:211 , SER A:212 , ASP A:215 , HOH A:560 , HOH A:908
BINDING SITE FOR RESIDUE GOL A 403
04
AC4
SOFTWARE
GLU A:7 , VAL A:8 , ARG A:9 , ARG A:380 , HOH A:671 , HOH A:967
BINDING SITE FOR RESIDUE GOL A 404
05
AC5
SOFTWARE
ASP A:206 , GLU A:232 , GLU A:258 , HOH A:950 , HOH A:951 , HOH A:952
BINDING SITE FOR RESIDUE MG A 405
06
AC6
SOFTWARE
SER A:247 , LEU A:250 , HOH A:949 , HOH A:964 , HOH A:965 , HOH A:966
BINDING SITE FOR RESIDUE MG A 406
07
AC7
SOFTWARE
ASP A:206 , ALA A:207 , HIS A:209 , GLU A:232 , GLU A:233
BINDING SITE FOR RESIDUE NA A 407
08
AC8
SOFTWARE
GLN A:238 , ALA A:260 , ALA A:261 , GLY A:262 , HIS A:266 , HOH A:830 , HOH A:831 , ALA B:260 , ALA B:261 , GLY B:262 , HIS B:266 , HOH B:631
BINDING SITE FOR RESIDUE PGE A 408
09
AC9
SOFTWARE
TRP A:179
BINDING SITE FOR RESIDUE EDO A 409
10
BC1
SOFTWARE
VAL A:6 , GLU A:7 , LYS A:67 , HOH A:614 , HOH A:671 , HOH A:809 , HOH A:918 , HOH A:967
BINDING SITE FOR RESIDUE EDO A 410
11
BC2
SOFTWARE
ARG A:90 , HIS B:24 , CYS B:139 , HIS B:171 , HIS B:209 , HIS B:309 , GOL B:404 , HOH B:530 , HOH B:569 , HOH B:598 , HOH B:711 , HOH B:938
BINDING SITE FOR RESIDUE TLA B 401
12
BC3
SOFTWARE
PRO B:181 , PHE B:208 , TYR B:211 , SER B:212 , ASP B:215 , HOH B:579 , HOH B:878 , HOH B:948
BINDING SITE FOR RESIDUE GOL B 402
13
BC4
SOFTWARE
TYR B:339 , GLY B:342 , HIS B:343 , HOH B:508 , HOH B:733 , HOH B:820 , HOH B:871 , HOH B:877
BINDING SITE FOR RESIDUE GOL B 403
14
BC5
SOFTWARE
HIS B:309 , ASN B:311 , GLU B:329 , GLY B:331 , LEU B:332 , TLA B:401 , HOH B:585 , HOH B:747 , HOH B:937
BINDING SITE FOR RESIDUE GOL B 404
15
BC6
SOFTWARE
GLU B:7 , VAL B:8 , ARG B:380 , HOH B:702
BINDING SITE FOR RESIDUE GOL B 405
16
BC7
SOFTWARE
ASP B:206 , GLU B:232 , GLU B:258 , HOH B:937 , HOH B:938 , HOH B:940
BINDING SITE FOR RESIDUE MG B 406
17
BC8
SOFTWARE
SER B:247 , LEU B:250 , HOH B:936 , HOH B:939 , HOH B:941 , HOH B:942
BINDING SITE FOR RESIDUE MG B 407
18
BC9
SOFTWARE
ASP B:206 , ALA B:207 , HIS B:209 , GLU B:232 , GLU B:233
BINDING SITE FOR RESIDUE NA B 408
19
CC1
SOFTWARE
LYS B:166 , ARG B:355 , ASP B:356 , HOH B:719 , HOH B:900
BINDING SITE FOR RESIDUE EDO B 410
[
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
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4hcha1 (A:-1-126)
1b: SCOP_d4hchb1 (B:-1-126)
2a: SCOP_d4hcha2 (A:127-382)
2b: SCOP_d4hchb2 (B:127-382)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Enolase N-terminal domain-like
(211)
Superfamily
:
Enolase N-terminal domain-like
(211)
Family
:
automated matches
(123)
Protein domain
:
automated matches
(123)
Agrobacterium tumefaciens [TaxId: 176299]
(6)
1a
d4hcha1
A:-1-126
1b
d4hchb1
B:-1-126
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
D-glucarate dehydratase-like
(65)
Protein domain
:
automated matches
(16)
Agrobacterium tumefaciens [TaxId: 176299]
(4)
2a
d4hcha2
A:127-382
2b
d4hchb2
B:127-382
[
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
Asymmetric Unit 2
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 (151 KB)
Header - Asym.Unit
Biol.Unit 1 (144 KB)
Header - Biol.Unit 1
Biol.Unit 2 (564 KB)
Header - Biol.Unit 2
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
4HCH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help