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.
4U4M
Asym. Unit
Info
Asym.Unit (188 KB)
Biol.Unit 1 (183 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 0.5M UREA UNFOLDED YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX WITH PYRUVATE
Authors
:
P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Date
:
24 Jul 14 (Deposition) - 29 Jul 15 (Release) - 29 Jul 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.09
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tim Barrel, Nal Superfamily, Kdga, Schiff Base, Catalytic Triad, Chemical Denaturant, Urea Promoted Unfolding, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Manoj Kumar, V. Bhaskar, S. Manicka, S. Krishnaswamy
Crystal Structure Of 0. 5M Urea Unfolded Yage, A Kdg Aldolas Protein In Complex With Pyruvate
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
2a: PYRUVIC ACID (PYRa)
2b: PYRUVIC ACID (PYRb)
2c: PYRUVIC ACID (PYRc)
2d: PYRUVIC ACID (PYRd)
3a: UREA (UREa)
3b: UREA (UREb)
3c: UREA (UREc)
3d: UREA (UREd)
3e: UREA (UREe)
3f: UREA (UREf)
3g: UREA (UREg)
3h: UREA (UREh)
3i: UREA (UREi)
3j: UREA (UREj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
2
PYR
4
Ligand/Ion
PYRUVIC ACID
3
URE
10
Ligand/Ion
UREA
[
close Hetero Component info
]
Sites
(22, 22)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:147 , THR A:176 , PHE A:265 , PYR A:404
binding site for residue URE A 401
02
AC2
SOFTWARE
ASP A:178 , TYR A:203 , ASP A:205 , PRO A:256 , ALA C:181 , ARG C:184
binding site for residue URE A 402
03
AC3
SOFTWARE
ASN A:93 , ARG A:95 , GLU A:96 , GLU A:99 , GLU B:67
binding site for residue URE A 403
04
AC4
SOFTWARE
PRO A:20 , PHE A:52 , GLY A:55 , SER A:56 , GLY A:57 , TYR A:145 , LYS A:174 , ILE A:219 , URE A:401
binding site for residue PYR A 404
05
AC5
SOFTWARE
LEU A:54 , PHE A:60 , GLY A:90 , VAL A:113 , ILE A:115 , TYR A:145
binding site for residue EDO A 407
06
AC6
SOFTWARE
ALA A:107
binding site for residue EDO A 408
07
AC7
SOFTWARE
GLY B:202 , TYR B:203 , ALA B:221 , PHE B:265 , PYR B:405
binding site for residue URE B 401
08
AC8
SOFTWARE
ARG B:73 , ASP B:77 , GLU C:293
binding site for residue URE B 402
09
AC9
SOFTWARE
LEU B:31 , GLU B:67
binding site for residue URE B 403
10
AD1
SOFTWARE
ARG A:129 , ASP B:262 , SER B:289 , PRO B:290
binding site for residue URE B 404
11
AD2
SOFTWARE
LEU B:54 , PHE B:60 , GLY B:88 , GLY B:90 , VAL B:113 , VAL B:114 , ILE B:115
binding site for residue EDO B 406
12
AD3
SOFTWARE
HIS B:283
binding site for residue EDO B 407
13
AD4
SOFTWARE
LYS B:191 , PRO B:195
binding site for residue EDO B 408
14
AD5
SOFTWARE
ASP B:77 , GLU C:271 , LYS C:296
binding site for residue URE C 401
15
AD6
SOFTWARE
PHE D:147 , THR D:176 , GLY D:202 , PHE D:265 , PYR D:403 , HOH D:501
binding site for residue URE D 401
16
AD7
SOFTWARE
ARG C:129 , ASP D:262 , SER D:289 , PRO D:290
binding site for residue URE D 402
17
AD8
SOFTWARE
LYS D:161 , ASP D:165
binding site for residue EDO D 404
18
AD9
SOFTWARE
ALA D:12
binding site for residue EDO D 405
19
AE1
SOFTWARE
GLY D:47 , VAL D:48 , ASP D:49
binding site for residue EDO D 406
20
AE2
SOFTWARE
PRO B:20 , PHE B:52 , GLY B:55 , SER B:56 , GLY B:57 , LEU B:144 , TYR B:145 , ASN B:146 , ILE B:173 , ASP B:175 , THR B:176 , LEU B:200 , ILE B:219 , URE B:401
binding site for Di-peptide PYR B 405 and LYS B 174
21
AE3
SOFTWARE
PRO C:20 , PHE C:52 , GLY C:55 , SER C:56 , GLY C:57 , LEU C:144 , TYR C:145 , ASN C:146 , ILE C:173 , ASP C:175 , THR C:176 , LEU C:200 , ILE C:219
binding site for Di-peptide PYR C 402 and LYS C 174
22
AE4
SOFTWARE
PRO D:20 , PHE D:52 , GLY D:55 , SER D:56 , GLY D:57 , LEU D:144 , TYR D:145 , ASN D:146 , ILE D:173 , ASP D:175 , THR D:176 , LEU D:200 , ILE D:219 , URE D:401
binding site for Di-peptide PYR D 403 and LYS D 174
[
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
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 (188 KB)
Header - Asym.Unit
Biol.Unit 1 (183 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
4U4M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help