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.
4ZOH
Biol. Unit 1
Info
Asym.Unit (204 KB)
Biol.Unit 1 (387 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 GLYCERALDEHYDE OXIDOREDUCTASE
Authors
:
H. Nishimasu, S. Fushinobu, T. Wakagi
Date
:
06 May 15 (Deposition) - 03 Feb 16 (Release) - 03 Feb 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Xanthine Oxidoreductase Family, Molybdopterin Cofactor, Flavin Adenine Dinucleotide, Iron-Sulfur Cluster, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Wakagi, H. Nishimasu, M. Miyake, S. Fushinobu
Archaeal Mo-Containing Glyceraldehyde Oxidoreductase Isozymes Exhibit Diverse Substrate Specificities Through Unique Subunit Assemblies.
Plos One V. 11 47333
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 22)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: ACETIC ACID (ACYa)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
5a: PTERIN CYTOSINE DINUCLEOTIDE (MCNa)
6a: MOLYBDENUM ATOM (MOa)
7a: DI(HYDROXYETHYL)ETHER (PEGa)
7b: DI(HYDROXYETHYL)ETHER (PEGb)
7c: DI(HYDROXYETHYL)ETHER (PEGc)
7d: DI(HYDROXYETHYL)ETHER (PEGd)
8a: TETRAETHYLENE GLYCOL (PG4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ACY
2
Ligand/Ion
ACETIC ACID
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
MCN
2
Ligand/Ion
PTERIN CYTOSINE DINUCLEOTIDE
6
MO
-1
Ligand/Ion
MOLYBDENUM ATOM
7
PEG
8
Ligand/Ion
DI(HYDROXYETHYL)ETHER
8
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:213 , ALA A:214 , PHE A:215 , ARG A:332 , HIS A:442 , GLY A:443 , GLN A:444 , ASP A:446 , ALA A:449 , TRP A:482 , GLY A:483 , SER A:484 , ARG A:485 , THR A:486 , VAL A:487 , VAL A:594 , THR A:596 , VAL A:597 , ILE A:598 , ASN A:599 , LEU A:602 , GLN A:606 , SER A:667 , LYS A:668 , GLY A:669 , ILE A:670 , GLY A:671 , GLU A:672 , MO A:802 , HOH A:943 , HOH A:1121 , HOH A:1219 , GLN C:105 , CYS C:143 , HOH C:357
binding site for residue MCN A 801
02
AC2
SOFTWARE
GLU A:672 , MCN A:801 , HOH A:913 , HOH A:1148 , HOH A:1219
binding site for residue MO A 802
03
AC3
SOFTWARE
TYR A:190 , ILE A:219 , ASP A:292 , ASP A:293 , GLY A:296 , ASN A:297 , TRP A:482 , HOH A:908 , HOH A:1112
binding site for residue 1PE A 803
04
AC4
SOFTWARE
GLU A:604 , ASP A:652 , TRP A:653 , TYR A:654 , HOH A:1026 , HOH A:1037 , HOH A:1134
binding site for residue PEG A 804
05
AC5
SOFTWARE
ARG B:28 , PRO B:29 , ALA B:31 , GLY B:32 , GLY B:33 , HIS B:34 , SER B:35 , LEU B:36 , HIS B:77 , ILE B:95 , GLY B:96 , VAL B:100 , GLY B:104 , THR B:105 , GLY B:108 , SER B:109 , SER B:111 , ALA B:117 , ASP B:118 , LEU B:160 , VAL B:161 , LYS B:178 , ASP B:185 , PHE B:186 , HOH B:420 , HOH B:432 , HOH B:440 , HOH B:465 , HOH B:489 , SER C:50
binding site for residue FAD B 301
06
AC6
SOFTWARE
THR B:168 , PHE B:169 , GLU B:170 , HOH B:500
binding site for residue PEG B 302
07
AC7
SOFTWARE
ASP A:106 , ASN B:79
binding site for residue PG4 B 303
08
AC8
SOFTWARE
SER B:81 , LYS B:82 , SER B:93 , ARG B:101
binding site for residue PEG B 304
09
AC9
SOFTWARE
TYR A:92 , MET B:1 , TYR B:2 , ARG B:43
binding site for residue ACY B 305
10
AD1
SOFTWARE
GLY C:46 , CYS C:47 , SER C:50 , CYS C:52 , GLY C:53 , CYS C:55 , CYS C:67
binding site for residue FES C 201
11
AD2
SOFTWARE
GLN C:105 , CYS C:106 , GLY C:107 , CYS C:109 , CYS C:141 , ARG C:142 , CYS C:143
binding site for residue FES C 202
12
AD3
SOFTWARE
ARG B:54 , ARG B:55 , ASN C:60 , GLU C:73 , ASP C:75 , GLY C:76 , HOH C:369
binding site for residue PEG C 203
[
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
(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
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 (204 KB)
Header - Asym.Unit
Biol.Unit 1 (387 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
4ZOH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
