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.
2X0N
Asym. Unit
Info
Asym.Unit (694 KB)
Biol.Unit 1 (456 KB)
Biol.Unit 2 (459 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM TRYPANOSOMA BRUCEI DETERMINED FROM LAUE DATA
Authors
:
F. M. D. Vellieux, J. Hajdu, W. G. J. Hol
Date
:
16 Dec 09 (Deposition) - 22 Dec 09 (Release) - 25 Jan 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,O,P,Q,R
Biol. Unit 1: A,B (2x)
Biol. Unit 2: O,P,Q,R (1x)
Keywords
:
Glycolysis, Glycosome, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. M. D. Vellieux, J. Hajdu, C. L. Verlinde, H. Groendijk, R. J. Read, T. J. Greenhough, J. W. Campbell, K. H. Kalk, J. A. Littlechild, H. C. Watson
Structure Of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase From Trypanosoma Brucei Determined From Laue Data.
Proc. Natl. Acad. Sci. Usa V. 90 2355 1993
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:196 , THR A:198 , NAD A:361
BINDING SITE FOR RESIDUE SO4 A 359
02
AC2
SOFTWARE
SER A:164 , THR A:225 , GLY A:226 , ALA A:227
BINDING SITE FOR RESIDUE SO4 A 360
03
AC3
SOFTWARE
GLY A:8 , GLY A:10 , ARG A:11 , ILE A:12 , ASP A:37 , MET A:38 , ALA A:89 , GLN A:90 , SER A:109 , THR A:110 , GLY A:111 , LEU A:112 , SER A:133 , ALA A:134 , CYS A:165 , ALA A:197 , ASN A:334 , SO4 A:359
BINDING SITE FOR RESIDUE NAD A 361
04
AC4
SOFTWARE
THR B:196 , THR B:198 , ARG B:248
BINDING SITE FOR RESIDUE SO4 B 359
05
AC5
SOFTWARE
SER B:164 , THR B:225 , GLY B:226 , ALA B:227
BINDING SITE FOR RESIDUE SO4 B 360
06
AC6
SOFTWARE
ASN B:7 , GLY B:8 , GLY B:10 , ARG B:11 , ILE B:12 , ASP B:37 , MET B:38 , ALA B:89 , GLN B:90 , SER B:109 , THR B:110 , GLY B:111 , LEU B:112 , SER B:133 , ALA B:134 , ALA B:197 , ASN B:334
BINDING SITE FOR RESIDUE NAD B 361
07
AC7
SOFTWARE
THR O:196 , THR O:198 , ARG O:248
BINDING SITE FOR RESIDUE SO4 O 359
08
AC8
SOFTWARE
SER O:164 , THR O:225 , GLY O:226 , ALA O:227
BINDING SITE FOR RESIDUE SO4 O 360
09
AC9
SOFTWARE
GLY O:8 , GLY O:10 , ARG O:11 , ILE O:12 , ASP O:37 , ALA O:89 , GLN O:90 , SER O:109 , THR O:110 , GLY O:111 , SER O:133 , ALA O:134 , CYS O:165 , ALA O:197 , ASN O:334 , TYR O:338
BINDING SITE FOR RESIDUE NAD O 361
10
BC1
SOFTWARE
THR P:196 , THR P:198 , ARG P:248
BINDING SITE FOR RESIDUE SO4 P 359
11
BC2
SOFTWARE
SER P:164 , THR P:225
BINDING SITE FOR RESIDUE SO4 P 360
12
BC3
SOFTWARE
GLY P:8 , GLY P:10 , ARG P:11 , ILE P:12 , VAL P:36 , ASP P:37 , MET P:38 , ALA P:89 , GLN P:90 , SER P:109 , THR P:110 , GLY P:111 , SER P:133 , ASN P:334 , TYR P:338
BINDING SITE FOR RESIDUE NAD P 361
13
BC4
SOFTWARE
THR Q:196 , THR Q:198 , ARG Q:248
BINDING SITE FOR RESIDUE SO4 Q 359
14
BC5
SOFTWARE
SER Q:164 , THR Q:225 , GLY Q:226 , ALA Q:227
BINDING SITE FOR RESIDUE SO4 Q 360
15
BC6
SOFTWARE
GLY Q:8 , GLY Q:10 , ARG Q:11 , ILE Q:12 , VAL Q:36 , ASP Q:37 , MET Q:38 , GLN Q:90 , SER Q:109 , THR Q:110 , GLY Q:111 , SER Q:133 , CYS Q:165 , ALA Q:197 , ASN Q:334 , TYR Q:338
BINDING SITE FOR RESIDUE NAD Q 361
16
BC7
SOFTWARE
THR R:196 , THR R:198 , ARG R:248 , NAD R:361
BINDING SITE FOR RESIDUE SO4 R 359
17
BC8
SOFTWARE
SER R:164 , THR R:225 , GLY R:226 , ALA R:227
BINDING SITE FOR RESIDUE SO4 R 360
18
BC9
SOFTWARE
GLY R:8 , GLY R:10 , ARG R:11 , ILE R:12 , VAL R:36 , ASP R:37 , MET R:38 , ALA R:89 , GLN R:90 , SER R:109 , THR R:110 , SER R:133 , ALA R:134 , CYS R:165 , ALA R:197 , ASN R:334 , TYR R:338 , SO4 R:359
BINDING SITE FOR RESIDUE NAD R 361
[
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, 6)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:163-170,B:163-170,O:163-170,P:16...)
;
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.
G3PG_TRYBB
164-171
6
A:163-170
B:163-170
O:163-170
P:163-170
Q:163-170
R:163-170
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d2x0na2 (A:165-333)
1b: SCOP_d2x0nb2 (B:165-333)
1c: SCOP_d2x0no2 (O:165-333)
1d: SCOP_d2x0np2 (P:165-333)
1e: SCOP_d2x0nq2 (Q:165-333)
1f: SCOP_d2x0nr2 (R:165-333)
2a: SCOP_d2x0na1 (A:1-164,A:334-358)
2b: SCOP_d2x0nb1 (B:1-164,B:334-358)
2c: SCOP_d2x0no1 (O:1-164,O:334-358)
2d: SCOP_d2x0np1 (P:1-164,P:334-358)
2e: SCOP_d2x0nq1 (Q:1-164,Q:334-358)
2f: SCOP_d2x0nr1 (R:1-164,R:334-358)
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)
Trypanosoma brucei brucei, glycosome [TaxId: 5702]
(1)
1a
d2x0na2
A:165-333
1b
d2x0nb2
B:165-333
1c
d2x0no2
O:165-333
1d
d2x0np2
P:165-333
1e
d2x0nq2
Q:165-333
1f
d2x0nr2
R:165-333
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)
Trypanosoma brucei brucei, glycosome [TaxId: 5702]
(1)
2a
d2x0na1
A:1-164,A:334-358
2b
d2x0nb1
B:1-164,B:334-358
2c
d2x0no1
O:1-164,O:334-358
2d
d2x0np1
P:1-164,P:334-358
2e
d2x0nq1
Q:1-164,Q:334-358
2f
d2x0nr1
R:1-164,R:334-358
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2x0nA02 (A:164-334)
1b: CATH_2x0nB02 (B:164-334)
1c: CATH_2x0nO02 (O:164-334)
1d: CATH_2x0nP02 (P:164-334)
1e: CATH_2x0nQ02 (Q:164-334)
1f: CATH_2x0nR02 (R:164-334)
2a: CATH_2x0nA01 (A:1-163,A:335-354)
2b: CATH_2x0nB01 (B:1-163,B:335-354)
2c: CATH_2x0nO01 (O:1-163,O:335-354)
2d: CATH_2x0nP01 (P:1-163,P:335-354)
2e: CATH_2x0nQ01 (Q:1-163,Q:335-354)
2f: CATH_2x0nR01 (R:1-163,R:335-354)
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)
Trypanosoma brucei brucei. Organism_taxid: 5702
(1)
1a
2x0nA02
A:164-334
1b
2x0nB02
B:164-334
1c
2x0nO02
O:164-334
1d
2x0nP02
P:164-334
1e
2x0nQ02
Q:164-334
1f
2x0nR02
R:164-334
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Trypanosoma brucei brucei. Organism_taxid: 5702
(1)
2a
2x0nA01
A:1-163,A:335-354
2b
2x0nB01
B:1-163,B:335-354
2c
2x0nO01
O:1-163,O:335-354
2d
2x0nP01
P:1-163,P:335-354
2e
2x0nQ01
Q:1-163,Q:335-354
2f
2x0nR01
R:1-163,R:335-354
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_2x0nR01 (R:170-332)
1b: PFAM_Gp_dh_C_2x0nR02 (R:170-332)
1c: PFAM_Gp_dh_C_2x0nR03 (R:170-332)
1d: PFAM_Gp_dh_C_2x0nR04 (R:170-332)
1e: PFAM_Gp_dh_C_2x0nR05 (R:170-332)
1f: PFAM_Gp_dh_C_2x0nR06 (R:170-332)
2a: PFAM_Gp_dh_N_2x0nR07 (R:2-165)
2b: PFAM_Gp_dh_N_2x0nR08 (R:2-165)
2c: PFAM_Gp_dh_N_2x0nR09 (R:2-165)
2d: PFAM_Gp_dh_N_2x0nR10 (R:2-165)
2e: PFAM_Gp_dh_N_2x0nR11 (R:2-165)
2f: PFAM_Gp_dh_N_2x0nR12 (R:2-165)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Trypanosoma brucei brucei
(1)
1a
Gp_dh_C-2x0nR01
R:170-332
1b
Gp_dh_C-2x0nR02
R:170-332
1c
Gp_dh_C-2x0nR03
R:170-332
1d
Gp_dh_C-2x0nR04
R:170-332
1e
Gp_dh_C-2x0nR05
R:170-332
1f
Gp_dh_C-2x0nR06
R:170-332
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Trypanosoma brucei brucei
(1)
2a
Gp_dh_N-2x0nR07
R:2-165
2b
Gp_dh_N-2x0nR08
R:2-165
2c
Gp_dh_N-2x0nR09
R:2-165
2d
Gp_dh_N-2x0nR10
R:2-165
2e
Gp_dh_N-2x0nR11
R:2-165
2f
Gp_dh_N-2x0nR12
R:2-165
[
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 O
Chain P
Chain Q
Chain R
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 (694 KB)
Header - Asym.Unit
Biol.Unit 1 (456 KB)
Header - Biol.Unit 1
Biol.Unit 2 (459 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
2X0N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help