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.
4I3X
Asym. Unit
Info
Asym.Unit (660 KB)
Biol.Unit 1 (172 KB)
Biol.Unit 2 (170 KB)
Biol.Unit 3 (168 KB)
Biol.Unit 4 (169 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 PHOSPHONOACETALDEHYDE DEHYDROGENASE IN COMPLEX WITH PHOSPHONOACETATE AND COFACTOR NAD+
Authors
:
S. K. Nair, V. Agarwal
Date
:
26 Nov 12 (Deposition) - 27 Nov 13 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.07
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,E (1x)
Biol. Unit 3: D,H (1x)
Biol. Unit 4: F,G (1x)
Keywords
:
Aldehyde Dehydrogenase, Phosphonate Catabolism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Agarwal, S. C. Peck, J. H. Chen, S. A. Borisova, J. R. Chekan, W. A. Van Der Donk, S. K. Nair
Structure And Function Of Phosphonoacetaldehyde Dehydrogenase: The Missing Link In Phosphonoacetate Formation.
Chem. Biol. V. 21 125 2014
[
close entry info
]
Hetero Components
(2, 16)
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)
1g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
1h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
2a: PHOSPHONOACETIC ACID (PAEa)
2b: PHOSPHONOACETIC ACID (PAEb)
2c: PHOSPHONOACETIC ACID (PAEc)
2d: PHOSPHONOACETIC ACID (PAEd)
2e: PHOSPHONOACETIC ACID (PAEe)
2f: PHOSPHONOACETIC ACID (PAEf)
2g: PHOSPHONOACETIC ACID (PAEg)
2h: PHOSPHONOACETIC ACID (PAEh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
PAE
8
Ligand/Ion
PHOSPHONOACETIC ACID
[
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
ILE A:154 , THR A:155 , PRO A:156 , PHE A:157 , ASN A:158 , LYS A:181 , THR A:183 , GLU A:184 , PRO A:214 , GLY A:218 , PHE A:232 , THR A:233 , GLY A:234 , SER A:235 , VAL A:238 , GLU A:254 , LEU A:255 , GLY A:256 , GLY A:257 , CYS A:291 , GLU A:385 , PHE A:387 , PHE A:453 , PAE A:502 , HOH A:686 , HOH A:720 , HOH A:834 , HOH A:935 , HOH A:947 , HOH A:1004
BINDING SITE FOR RESIDUE NAD A 501
02
AC2
SOFTWARE
ARG A:108 , ASN A:158 , HIS A:159 , ARG A:290 , CYS A:291 , THR A:292 , ARG A:447 , NAD A:501 , HOH A:627 , HOH A:719 , HOH A:723 , HOH A:1070
BINDING SITE FOR RESIDUE PAE A 502
03
AC3
SOFTWARE
ILE B:154 , THR B:155 , PRO B:156 , PHE B:157 , ASN B:158 , LYS B:181 , THR B:183 , GLU B:184 , PRO B:214 , GLY B:218 , PHE B:232 , THR B:233 , GLY B:234 , SER B:235 , VAL B:238 , GLU B:254 , LEU B:255 , GLY B:256 , GLY B:257 , CYS B:291 , GLU B:385 , PHE B:387 , PHE B:453 , PAE B:502 , HOH B:632 , HOH B:676 , HOH B:843 , HOH B:899
BINDING SITE FOR RESIDUE NAD B 501
04
AC4
SOFTWARE
ARG B:108 , ASN B:158 , HIS B:159 , ARG B:290 , CYS B:291 , ARG B:447 , NAD B:501 , HOH B:621 , HOH B:648 , HOH B:961 , HOH B:978
BINDING SITE FOR RESIDUE PAE B 502
05
AC5
SOFTWARE
ILE C:154 , THR C:155 , PRO C:156 , PHE C:157 , ASN C:158 , LYS C:181 , THR C:183 , GLU C:184 , PRO C:214 , GLY C:218 , PHE C:232 , THR C:233 , GLY C:234 , SER C:235 , VAL C:238 , GLU C:254 , LEU C:255 , GLY C:256 , GLY C:257 , CYS C:291 , GLU C:385 , PHE C:387 , PHE C:453 , PAE C:502 , HOH C:642 , HOH C:702 , HOH C:713 , HOH C:770 , HOH C:779 , HOH C:929
BINDING SITE FOR RESIDUE NAD C 501
06
AC6
SOFTWARE
ARG C:108 , ASN C:158 , HIS C:159 , ARG C:290 , CYS C:291 , THR C:292 , ARG C:447 , NAD C:501 , HOH C:606
BINDING SITE FOR RESIDUE PAE C 502
07
AC7
SOFTWARE
ILE D:154 , THR D:155 , PRO D:156 , PHE D:157 , ASN D:158 , LYS D:181 , THR D:183 , GLU D:184 , PRO D:214 , GLY D:218 , PHE D:232 , THR D:233 , GLY D:234 , SER D:235 , VAL D:238 , LEU D:241 , GLU D:254 , LEU D:255 , GLY D:256 , GLY D:257 , CYS D:291 , GLU D:385 , PHE D:387 , PHE D:453 , PAE D:502 , HOH D:645 , HOH D:700 , HOH D:807
BINDING SITE FOR RESIDUE NAD D 501
08
AC8
SOFTWARE
ARG D:108 , ASN D:158 , HIS D:159 , ARG D:290 , CYS D:291 , ARG D:447 , NAD D:501 , HOH D:624 , HOH D:719
BINDING SITE FOR RESIDUE PAE D 502
09
AC9
SOFTWARE
ILE E:154 , THR E:155 , PRO E:156 , PHE E:157 , ASN E:158 , LYS E:181 , THR E:183 , GLU E:184 , GLY E:218 , PHE E:232 , THR E:233 , GLY E:234 , SER E:235 , VAL E:238 , LEU E:241 , GLU E:254 , LEU E:255 , GLY E:256 , GLY E:257 , CYS E:291 , GLU E:385 , PHE E:387 , PHE E:453 , PAE E:502 , HOH E:644 , HOH E:691 , HOH E:765 , HOH E:783 , HOH E:793
BINDING SITE FOR RESIDUE NAD E 501
10
BC1
SOFTWARE
ARG E:108 , ASN E:158 , HIS E:159 , ARG E:290 , CYS E:291 , THR E:292 , ARG E:447 , NAD E:501 , HOH E:628 , HOH E:679
BINDING SITE FOR RESIDUE PAE E 502
11
BC2
SOFTWARE
ILE F:154 , THR F:155 , PRO F:156 , PHE F:157 , LYS F:181 , THR F:183 , GLU F:184 , GLY F:218 , PHE F:232 , THR F:233 , GLY F:234 , SER F:235 , VAL F:238 , LEU F:241 , GLU F:254 , LEU F:255 , GLY F:256 , GLY F:257 , CYS F:291 , GLU F:385 , PHE F:387 , PHE F:453 , PAE F:502 , HOH F:617 , HOH F:724 , HOH F:821 , HOH F:826
BINDING SITE FOR RESIDUE NAD F 501
12
BC3
SOFTWARE
ARG F:108 , ASN F:158 , HIS F:159 , ARG F:290 , CYS F:291 , THR F:292 , ARG F:447 , NAD F:501 , HOH F:675 , HOH F:758 , HOH F:775
BINDING SITE FOR RESIDUE PAE F 502
13
BC4
SOFTWARE
ILE G:154 , THR G:155 , PRO G:156 , PHE G:157 , LYS G:181 , THR G:183 , GLU G:184 , PRO G:214 , GLY G:218 , PHE G:232 , THR G:233 , GLY G:234 , SER G:235 , VAL G:238 , LEU G:241 , GLU G:254 , LEU G:255 , GLY G:256 , GLY G:257 , CYS G:291 , GLU G:385 , PHE G:387 , PHE G:453 , PAE G:502 , HOH G:695 , HOH G:844 , HOH G:897 , HOH G:932
BINDING SITE FOR RESIDUE NAD G 501
14
BC5
SOFTWARE
ARG G:108 , HIS G:159 , ARG G:290 , CYS G:291 , THR G:292 , ARG G:447 , NAD G:501 , HOH G:624 , HOH G:696 , HOH G:760
BINDING SITE FOR RESIDUE PAE G 502
15
BC6
SOFTWARE
ILE H:154 , THR H:155 , PRO H:156 , PHE H:157 , ASN H:158 , LYS H:181 , THR H:183 , GLU H:184 , GLY H:218 , PHE H:232 , THR H:233 , GLY H:234 , SER H:235 , VAL H:238 , LEU H:241 , GLU H:254 , LEU H:255 , GLY H:256 , GLY H:257 , CYS H:291 , GLU H:385 , PHE H:387 , PHE H:453 , PAE H:502 , HOH H:669 , HOH H:716
BINDING SITE FOR RESIDUE NAD H 501
16
BC7
SOFTWARE
ARG H:108 , ASN H:158 , HIS H:159 , ARG H:290 , CYS H:291 , ARG H:447 , NAD H:501 , HOH H:668 , HOH H:833
BINDING SITE FOR RESIDUE PAE H 502
[
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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d4i3xa_ (A:)
1b: SCOP_d4i3xb_ (B:)
1c: SCOP_d4i3xc_ (C:)
1d: SCOP_d4i3xd_ (D:)
1e: SCOP_d4i3xe_ (E:)
1f: SCOP_d4i3xf_ (F:)
1g: SCOP_d4i3xg_ (G:)
1h: SCOP_d4i3xh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ALDH-like
(168)
Superfamily
:
ALDH-like
(168)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Sinorhizobium meliloti [TaxId: 266834]
(9)
1a
d4i3xa_
A:
1b
d4i3xb_
B:
1c
d4i3xc_
C:
1d
d4i3xd_
D:
1e
d4i3xe_
E:
1f
d4i3xf_
F:
1g
d4i3xg_
G:
1h
d4i3xh_
H:
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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 (660 KB)
Header - Asym.Unit
Biol.Unit 1 (172 KB)
Header - Biol.Unit 1
Biol.Unit 2 (170 KB)
Header - Biol.Unit 2
Biol.Unit 3 (168 KB)
Header - Biol.Unit 3
Biol.Unit 4 (169 KB)
Header - Biol.Unit 4
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
4I3X
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help