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.
3CIF
Asym. Unit
Info
Asym.Unit (229 KB)
Biol.Unit 1 (221 KB)
Biol.Unit 2 (114 KB)
Biol.Unit 3 (113 KB)
Biol.Unit 4 (114 KB)
Biol.Unit 5 (113 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 C153S MUTANT GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM
Authors
:
W. J. Cook, O. Senkovich, D. Chattopadhyay
Date
:
11 Mar 08 (Deposition) - 24 Mar 09 (Release) - 18 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: B,C (1x)
Biol. Unit 5: A,D (1x)
Keywords
:
Dehyrogenase Glyceraldehyde 3-Phosphate, Glycolysis, Glycolytic Enzyme, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. J. Cook, O. Senkovich, D. Chattopadhyay
An Unexpected Phosphate Binding Site In Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal Structures Of Apo, Holo And Ternary Complex Of Cryptosporidium Parvum Enzyme
Bmc Struct. Biol. V. 9 9 2009
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: GLYCERALDEHYDE-3-PHOSPHATE (G3Ha)
1b: GLYCERALDEHYDE-3-PHOSPHATE (G3Hb)
1c: GLYCERALDEHYDE-3-PHOSPHATE (G3Hc)
1d: GLYCERALDEHYDE-3-PHOSPHATE (G3Hd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G3H
4
Ligand/Ion
GLYCERALDEHYDE-3-PHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:152 , SER A:153 , THR A:154 , HIS A:180 , THR A:183 , THR A:214 , GLY A:215 , ALA A:216 , ARG A:237 , ASN A:319 , HOH A:407 , HOH A:423 , HOH A:491 , HOH A:699 , NAD A:5463
BINDING SITE FOR RESIDUE G3H A 1337
02
AC2
SOFTWARE
SER B:152 , SER B:153 , THR B:154 , HIS B:180 , THR B:183 , THR B:214 , GLY B:215 , ALA B:216 , ARG B:237 , HOH B:364 , HOH B:412 , HOH B:634 , HOH B:700 , NAD B:5464
BINDING SITE FOR RESIDUE G3H B 1338
03
AC3
SOFTWARE
SER D:152 , SER D:153 , THR D:154 , HIS D:180 , ARG D:237 , MG D:340 , HOH D:384 , HOH D:430 , NAD D:5466
BINDING SITE FOR RESIDUE G3H D 1340
04
AC4
SOFTWARE
ASN A:8 , GLY A:9 , GLY A:11 , ARG A:12 , ILE A:13 , ASN A:33 , ASP A:34 , PRO A:35 , PHE A:36 , MET A:37 , ALA A:78 , LYS A:79 , SER A:97 , THR A:98 , GLY A:99 , PHE A:101 , SER A:121 , ALA A:122 , ALA A:184 , ASN A:319 , TYR A:323 , HOH A:340 , HOH A:343 , HOH A:346 , HOH A:350 , HOH A:356 , HOH A:386 , HOH A:408 , HOH A:446 , HOH A:453 , G3H A:1337
BINDING SITE FOR RESIDUE NAD A 5463
05
AC5
SOFTWARE
ASN B:8 , GLY B:9 , GLY B:11 , ARG B:12 , ILE B:13 , ASN B:33 , ASP B:34 , PRO B:35 , PHE B:36 , MET B:37 , ALA B:78 , LYS B:79 , SER B:97 , THR B:98 , GLY B:99 , PHE B:101 , SER B:121 , ALA B:122 , ALA B:184 , ASN B:319 , TYR B:323 , HOH B:342 , HOH B:345 , HOH B:346 , HOH B:348 , HOH B:355 , HOH B:356 , HOH B:369 , HOH B:373 , HOH B:394 , HOH B:548 , HOH B:720 , G3H B:1338 , HOH C:410
BINDING SITE FOR RESIDUE NAD B 5464
06
AC6
SOFTWARE
ASN C:8 , GLY C:9 , GLY C:11 , ARG C:12 , ILE C:13 , ASN C:33 , ASP C:34 , PRO C:35 , PHE C:36 , MET C:37 , ALA C:78 , LYS C:79 , SER C:97 , THR C:98 , GLY C:99 , PHE C:101 , SER C:121 , ALA C:122 , ALA C:184 , ASN C:319 , TYR C:323 , GOL C:340 , HOH C:347 , HOH C:350 , HOH C:358 , HOH C:365 , HOH C:372 , HOH C:388 , HOH C:393 , HOH C:440 , HOH C:484 , HOH C:704 , HOH C:705 , HOH C:706 , G3H C:1339
BINDING SITE FOR RESIDUE NAD C 5465
07
AC7
SOFTWARE
ASN D:8 , GLY D:9 , GLY D:11 , ARG D:12 , ILE D:13 , ASN D:33 , ASP D:34 , PRO D:35 , PHE D:36 , MET D:37 , ALA D:78 , LYS D:79 , SER D:97 , THR D:98 , GLY D:99 , PHE D:101 , SER D:121 , ALA D:122 , ALA D:184 , ASN D:319 , TYR D:323 , HOH D:354 , HOH D:355 , HOH D:369 , HOH D:370 , HOH D:371 , HOH D:384 , HOH D:423 , HOH D:430 , HOH D:438 , HOH D:483 , G3H D:1340
BINDING SITE FOR RESIDUE NAD D 5466
08
AC8
SOFTWARE
PHE C:36 , HOH C:544 , NAD C:5465
BINDING SITE FOR RESIDUE GOL C 340
09
AC9
SOFTWARE
ASP B:288 , CYS B:292
BINDING SITE FOR RESIDUE GOL B 340
10
BC1
SOFTWARE
CYS B:21 , ARG B:24 , ILE B:27
BINDING SITE FOR RESIDUE MG B 341
11
BC2
SOFTWARE
SER C:152 , SER C:153 , THR C:154 , HIS C:180 , THR C:183 , THR C:214 , ALA C:216 , ARG C:237 , HOH C:527 , HOH C:687 , HOH C:701 , HOH C:702 , NAD C:5465
BINDING SITE FOR RESIDUE G3H C 1339
12
BC3
SOFTWARE
THR D:154 , THR D:214 , HOH D:342 , G3H D:1340
BINDING SITE FOR RESIDUE MG D 340
[
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
(2, 8)
Info
all CATH domains
1a: CATH_3cifA02 (A:151-319)
1b: CATH_3cifC02 (C:151-319)
1c: CATH_3cifD02 (D:151-319)
1d: CATH_3cifB02 (B:151-319)
2a: CATH_3cifA01 (A:2-150,A:320-339)
2b: CATH_3cifB01 (B:2-150,B:320-339)
2c: CATH_3cifC01 (C:2-150,C:320-339)
2d: CATH_3cifD01 (D:2-150,D:320-339)
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)
Cryptosporidium parvum. Organism_taxid: 5807.
(3)
1a
3cifA02
A:151-319
1b
3cifC02
C:151-319
1c
3cifD02
D:151-319
1d
3cifB02
B:151-319
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Cryptosporidium parvum. Organism_taxid: 5807.
(5)
2a
3cifA01
A:2-150,A:320-339
2b
3cifB01
B:2-150,B:320-339
2c
3cifC01
C:2-150,C:320-339
2d
3cifD01
D:2-150,D:320-339
[
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 (229 KB)
Header - Asym.Unit
Biol.Unit 1 (221 KB)
Header - Biol.Unit 1
Biol.Unit 2 (114 KB)
Header - Biol.Unit 2
Biol.Unit 3 (113 KB)
Header - Biol.Unit 3
Biol.Unit 4 (114 KB)
Header - Biol.Unit 4
Biol.Unit 5 (113 KB)
Header - Biol.Unit 5
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
3CIF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
