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.
4R41
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (119 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLEX CRYSTAL STRUCTURE OF 4-NITRO-2-PHOSPHONO-BENZOIC ACID WITH SP-ASPARTATE-SEMIALDEHYDE DEHYDROGENASE AND NICOTINAMIDE-DINUCLEOTIDE
Authors
:
A. G. Pavlovsky, R. E. Viola
Date
:
18 Aug 14 (Deposition) - 10 Dec 14 (Release) - 31 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.61
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, Dehydrogenase, Oxidoreductase, Nadp Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Pavlovsky, B. Thangavelu, P. Bhansali, R. E. Viola
A Cautionary Tale Of Structure-Guided Inhibitor Development Against An Essential Enzyme In The Aspartate-Biosynthetic Pathway.
Acta Crystallogr. , Sect. D V. 70 3244 2014
[
close entry info
]
Hetero Components
(5, 16)
Info
All Hetero Components
1a: 4-NITRO-2-PHOSPHONOBENZOIC ACID (4NOa)
1b: 4-NITRO-2-PHOSPHONOBENZOIC ACID (4NOb)
2a: ACETATE ION (ACTa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
5a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
5b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4NO
2
Ligand/Ion
4-NITRO-2-PHOSPHONOBENZOIC ACID
2
ACT
1
Ligand/Ion
ACETATE ION
3
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
4
NA
3
Ligand/Ion
SODIUM ION
5
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:14 , SER A:71 , ALA A:72 , GLY A:73 , SER A:74 , ASN A:94 , THR A:95 , SER A:96 , ARG A:99 , ASN A:127 , LYS A:223
BINDING SITE FOR RESIDUE 4NO A 401
02
AC2
SOFTWARE
GLY A:9 , THR A:11 , GLY A:12 , ALA A:13 , ALA A:36 , SER A:37 , ARG A:39 , SER A:40 , THR A:57 , ALA A:72 , GLY A:161 , MET A:162 , GLY A:163 , LEU A:166 , HOH A:598 , HOH A:648
BINDING SITE FOR RESIDUE NAP A 402
03
AC3
SOFTWARE
VAL A:111 , HIS A:114 , ILE A:231 , MET A:232
BINDING SITE FOR RESIDUE ACT A 403
04
AC4
SOFTWARE
ILE A:273 , ALA A:274 , PHE A:276 , ALA A:279 , HOH A:614 , GLU B:343
BINDING SITE FOR RESIDUE NA A 404
05
AC5
SOFTWARE
GLU A:343 , HOH A:632 , ILE B:273 , ALA B:274 , PHE B:276 , ALA B:279
BINDING SITE FOR RESIDUE NA A 405
06
AC6
SOFTWARE
SER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , LEU A:327 , HOH A:585
BINDING SITE FOR RESIDUE EDO A 406
07
AC7
SOFTWARE
GLU A:282 , PRO A:291 , GLN A:292 , ASN A:295 , ALA A:296 , PHE A:303
BINDING SITE FOR RESIDUE EDO A 407
08
AC8
SOFTWARE
LYS A:229 , ASP B:312 , HOH B:534
BINDING SITE FOR RESIDUE EDO A 408
09
AC9
SOFTWARE
GLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:503
BINDING SITE FOR RESIDUE EDO A 409
10
BC1
SOFTWARE
LEU A:311 , ASP A:312 , HOH A:561 , LYS B:229
BINDING SITE FOR RESIDUE EDO A 410
11
BC2
SOFTWARE
SER B:71 , ALA B:72 , GLY B:73 , SER B:74 , ASN B:94 , SER B:96 , ARG B:99 , ASN B:127 , LYS B:223
BINDING SITE FOR RESIDUE 4NO B 401
12
BC3
SOFTWARE
GLY B:9 , THR B:11 , GLY B:12 , ALA B:13 , ALA B:36 , SER B:37 , ARG B:39 , SER B:40 , LYS B:43 , THR B:57 , ALA B:72 , THR B:76 , GLY B:161 , MET B:162 , GLY B:163 , HOH B:587 , HOH B:606 , HOH B:611
BINDING SITE FOR RESIDUE NAP B 402
13
BC4
SOFTWARE
ASP B:147 , SER B:236 , HOH B:558 , HOH B:567 , HOH B:619
BINDING SITE FOR RESIDUE NA B 403
14
BC5
SOFTWARE
SER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:555
BINDING SITE FOR RESIDUE EDO B 404
15
BC6
SOFTWARE
GLU B:282 , PRO B:291 , GLN B:292 , ASN B:295 , PHE B:303 , HOH B:518
BINDING SITE FOR RESIDUE EDO B 405
16
BC7
SOFTWARE
ASP A:312 , ARG B:148 , HOH B:567
BINDING SITE FOR RESIDUE EDO B 406
[
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
(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
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 (125 KB)
Header - Asym.Unit
Biol.Unit 1 (119 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
4R41
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help