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.
1I32
Biol. Unit 2
Info
Asym.Unit (356 KB)
Biol.Unit 1 (235 KB)
Biol.Unit 2 (233 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LEISHMANIA MEXICANA GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH INHIBITORS
Authors
:
S. Suresh, J. C. Bressi, K. J. Kennedy, C. L. M. J. Verlinde, M. H. Gelb, W. G. J. Hol
Date
:
12 Feb 01 (Deposition) - 03 Oct 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F (2x)
Keywords
:
Enzyme, Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Suresh, J. C. Bressi, K. J. Kennedy, C. L. Verlinde, M. H. Gelb, W. G. Hol
Conformational Changes In Leishmania Mexicana Glyceraldehyde-3-Phosphate Dehydrogenase Induced By Designed Inhibitors.
J. Mol. Biol. V. 309 423 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDa)
1b: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDb)
1c: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDc)
1d: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDd)
1e: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDe)
1f: N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DI... (NMDf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NMD
4
Ligand/Ion
N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DIMETHOXYBENZAMIDO]-2'-DEOXY-ADENOSINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ASN E:8 , GLY E:9 , GLY E:11 , ASP E:38 , MET E:39 , SER E:40 , ALA E:90 , GLN E:91 , ARG E:92 , THR E:111 , LEU E:113 , HOH E:599 , VAL F:206
BINDING SITE FOR RESIDUE NMD E 365
2
AC6
SOFTWARE
VAL E:206 , ASN F:8 , GLY F:9 , GLY F:11 , ASP F:38 , MET F:39 , SER F:40 , ALA F:90 , GLN F:91 , SER F:110 , THR F:111 , LEU F:113 , HOH F:651 , HOH F:980
BINDING SITE FOR RESIDUE NMD F 366
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (E:164-171,F:164-171)
;
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_LEIME
165-172
4
-
-
-
-
E:164-171
F:164-171
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d1i32a2 (A:166-334)
1b: SCOP_d1i32b2 (B:166-334)
1c: SCOP_d1i32c2 (C:166-334)
1d: SCOP_d1i32d2 (D:166-334)
1e: SCOP_d1i32e2 (E:166-334)
1f: SCOP_d1i32f2 (F:166-334)
2a: SCOP_d1i32a1 (A:1-165,A:335-358)
2b: SCOP_d1i32b1 (B:1-165,B:335-358)
2c: SCOP_d1i32c1 (C:1-165,C:335-358)
2d: SCOP_d1i32d1 (D:1-165,D:335-358)
2e: SCOP_d1i32e1 (E:1-165,E:335-358)
2f: SCOP_d1i32f1 (F:1-165,F:335-358)
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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(5)
1a
d1i32a2
A:166-334
1b
d1i32b2
B:166-334
1c
d1i32c2
C:166-334
1d
d1i32d2
D:166-334
1e
d1i32e2
E:166-334
1f
d1i32f2
F:166-334
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)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(5)
2a
d1i32a1
A:1-165,A:335-358
2b
d1i32b1
B:1-165,B:335-358
2c
d1i32c1
C:1-165,C:335-358
2d
d1i32d1
D:1-165,D:335-358
2e
d1i32e1
E:1-165,E:335-358
2f
d1i32f1
F:1-165,F:335-358
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1i32A02 (A:165-335)
1b: CATH_1i32B02 (B:165-335)
1c: CATH_1i32C02 (C:165-335)
1d: CATH_1i32D02 (D:165-335)
1e: CATH_1i32E02 (E:165-335)
1f: CATH_1i32F02 (F:165-335)
2a: CATH_1i32A01 (A:2-164,A:336-355)
2b: CATH_1i32D01 (D:2-164,D:336-355)
2c: CATH_1i32E01 (E:2-164,E:336-355)
2d: CATH_1i32F01 (F:2-164,F:336-355)
2e: CATH_1i32B01 (B:2-164,B:336-355)
2f: CATH_1i32C01 (C:2-164,C:336-355)
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)
Leishmania mexicana. Organism_taxid: 5665.
(2)
1a
1i32A02
A:165-335
1b
1i32B02
B:165-335
1c
1i32C02
C:165-335
1d
1i32D02
D:165-335
1e
1i32E02
E:165-335
1f
1i32F02
F:165-335
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Leishmania mexicana. Organism_taxid: 5665.
(8)
2a
1i32A01
A:2-164,A:336-355
2b
1i32D01
D:2-164,D:336-355
2c
1i32E01
E:2-164,E:336-355
2d
1i32F01
F:2-164,F:336-355
2e
1i32B01
B:2-164,B:336-355
2f
1i32C01
C:2-164,C:336-355
[
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 E
Chain F
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 (356 KB)
Header - Asym.Unit
Biol.Unit 1 (235 KB)
Header - Biol.Unit 1
Biol.Unit 2 (233 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
1I32
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help