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.
2CZC
Asym. Unit
Info
Asym.Unit (230 KB)
Biol.Unit 1 (224 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-3-PHOSPHATE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII OT3
Authors
:
K. Ito, R. Arai, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama, Riken Str Genomics/Proteomics Initiative (Rsgi)
Date
:
13 Jul 05 (Deposition) - 13 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Glycolysis, Nad, Oxidoreductase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Ito, R. Arai, T. Kamo-Uchikubo, M. Shirouzu, S. Yokoyama
Crystal Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase From Pyrococcus Horikoshii Ot3
To Be Published
[
close entry info
]
Hetero Components
(2, 9)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
PO4
5
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:140 , CYS A:141 , ASN A:142 , ARG A:166 , HIS A:191 , HIS A:192 , HOH A:644 , HOH A:746
BINDING SITE FOR RESIDUE PO4 A 601
2
AC2
SOFTWARE
ARG A:166 , ARG A:167 , ALA A:168 , ARG A:176 , HOH A:737
BINDING SITE FOR RESIDUE PO4 A 602
3
AC3
SOFTWARE
SER B:140 , CYS B:141 , ASN B:142 , ARG B:166 , HIS B:191 , HIS B:192 , HOH B:691
BINDING SITE FOR RESIDUE PO4 B 603
4
AC4
SOFTWARE
SER C:140 , CYS C:141 , ASN C:142 , ARG C:166 , HIS C:191 , HIS C:192 , HOH C:679 , HOH C:681 , HOH C:703
BINDING SITE FOR RESIDUE PO4 C 604
5
AC5
SOFTWARE
SER D:140 , CYS D:141 , ASN D:142 , HIS D:191 , HIS D:192 , HOH D:653
BINDING SITE FOR RESIDUE PO4 D 605
6
AC6
SOFTWARE
ASN A:8 , TYR A:10 , GLY A:11 , THR A:12 , ILE A:13 , THR A:35 , ALA A:54 , ALA A:86 , THR A:87 , PRO A:88 , GLN A:109 , GLY A:111 , CYS A:141 , ARG A:167 , ASP A:170 , GLN A:298 , HOH A:614 , HOH A:621 , HOH A:625 , HOH A:682 , HOH A:747 , HOH A:749
BINDING SITE FOR RESIDUE NAD A 501
7
AC7
SOFTWARE
ASN B:8 , GLY B:9 , TYR B:10 , GLY B:11 , THR B:12 , ILE B:13 , THR B:35 , ALA B:54 , ALA B:86 , THR B:87 , PRO B:88 , GLN B:109 , GLY B:111 , CYS B:141 , ARG B:167 , ASP B:170 , GLN B:298 , HOH B:617 , HOH B:640 , HOH B:650 , HOH B:672 , HOH B:726 , HOH B:728
BINDING SITE FOR RESIDUE NAD B 502
8
AC8
SOFTWARE
ASN C:8 , GLY C:9 , TYR C:10 , GLY C:11 , THR C:12 , ILE C:13 , ALA C:86 , THR C:87 , GLN C:109 , GLY C:111 , CYS C:141 , ARG C:167 , ASP C:170 , GLN C:298 , HOH C:613 , HOH C:643 , HOH C:679 , HOH C:710 , HOH C:714 , HOH C:715 , HOH C:716
BINDING SITE FOR RESIDUE NAD C 503
9
AC9
SOFTWARE
ASN D:8 , TYR D:10 , GLY D:11 , THR D:12 , ILE D:13 , ALA D:54 , ALA D:86 , THR D:87 , PRO D:88 , GLY D:89 , GLN D:109 , GLY D:111 , CYS D:141 , ARG D:167 , ASP D:170 , GLN D:298 , HOH D:610 , HOH D:642 , HOH D:675 , HOH D:695 , HOH D:696
BINDING SITE FOR RESIDUE NAD D 504
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:139-146,B:139-146,C:139-146,D:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3P_PYRHO
139-146
4
A:139-146
B:139-146
C:139-146
D:139-146
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d2czca1 (A:140-301)
1b: SCOP_d2czcb2 (B:140-301)
1c: SCOP_d2czcc2 (C:140-301)
1d: SCOP_d2czcd2 (D:140-301)
2a: SCOP_d2czca2 (A:1-139,A:302-334)
2b: SCOP_d2czcb1 (B:2-139,B:302-334)
2c: SCOP_d2czcc1 (C:2-139,C:302-334)
2d: SCOP_d2czcd1 (D:2-139,D:302-333)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Pyrococcus horikoshii [TaxId: 53953]
(1)
1a
d2czca1
A:140-301
1b
d2czcb2
B:140-301
1c
d2czcc2
C:140-301
1d
d2czcd2
D:140-301
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
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Pyrococcus horikoshii [TaxId: 53953]
(1)
2a
d2czca2
A:1-139,A:302-334
2b
d2czcb1
B:2-139,B:302-334
2c
d2czcc1
C:2-139,C:302-334
2d
d2czcd1
D:2-139,D:302-333
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2czcA02 (A:140-301)
1b: CATH_2czcB02 (B:140-301)
1c: CATH_2czcC02 (C:140-301)
1d: CATH_2czcD02 (D:140-301)
2a: CATH_2czcA01 (A:1-139,A:302-334)
2b: CATH_2czcB01 (B:2-139,B:302-334)
2c: CATH_2czcC01 (C:2-139,C:302-334)
2d: CATH_2czcD01 (D:2-139,D:302-333)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(1)
1a
2czcA02
A:140-301
1b
2czcB02
B:140-301
1c
2czcC02
C:140-301
1d
2czcD02
D:140-301
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(4)
2a
2czcA01
A:1-139,A:302-334
2b
2czcB01
B:2-139,B:302-334
2c
2czcC01
C:2-139,C:302-334
2d
2czcD01
D:2-139,D:302-333
[
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 (230 KB)
Header - Asym.Unit
Biol.Unit 1 (224 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
2CZC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help