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.
1C1D
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (125 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE
Authors
:
J. L. Vanhooke, J. B. Thoden
Date
:
21 Jul 99 (Deposition) - 30 Aug 00 (Release) - 30 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Amino Acid Dehydrogenase, Oxidative Deamination Mechanism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. M. Brunhuber, J. B. Thoden, J. S. Blanchard, J. L. Vanhooke
Rhodococcus L-Phenylalanine Dehydrogenase: Kinetics, Mechanism, And Structural Basis For Catalytic Specificity.
Biochemistry V. 39 9174 2000
[
close entry info
]
Hetero Components
(6, 12)
Info
All Hetero Components
1a: ISOPROPYL ALCOHOL (IPAa)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
4a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
4b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
5a: PHENYLALANINE (PHEa)
5b: PHENYLALANINE (PHEb)
6a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IPA
1
Ligand/Ion
ISOPROPYL ALCOHOL
2
K
4
Ligand/Ion
POTASSIUM ION
3
NA
2
Ligand/Ion
SODIUM ION
4
NAI
2
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
5
PHE
2
Mod. Amino Acid
PHENYLALANINE
6
PO4
1
Ligand/Ion
PHOSPHATE ION
[
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
ASP A:118 , THR A:121 , HOH A:1493 , HOH A:1602
BINDING SITE FOR RESIDUE K A 850
02
AC2
SOFTWARE
LEU B:170 , SER B:172 , ASP B:174 , LEU B:176 , PO4 B:880 , HOH B:1194 , HOH B:1421
BINDING SITE FOR RESIDUE K B 851
03
AC3
SOFTWARE
ASP B:118 , THR B:121 , HOH B:1320 , HOH B:1452 , HOH B:1667 , HOH B:1746
BINDING SITE FOR RESIDUE K B 852
04
AC4
SOFTWARE
VAL A:136 , PHE A:137 , GLY A:138 , ARG A:139 , GLY A:145 , GLU A:299
BINDING SITE FOR RESIDUE K A 853
05
AC5
SOFTWARE
ASP B:30 , HOH B:1094 , HOH B:1140
BINDING SITE FOR RESIDUE NA B 854
06
AC6
SOFTWARE
GLN B:200 , LEU B:201 , HIS B:219 , HOH B:1067 , HOH B:1754
BINDING SITE FOR RESIDUE NA B 855
07
AC7
SOFTWARE
SER B:1 , SER B:4 , THR B:54 , LYS B:58 , LEU B:170 , LEU B:176 , K B:851 , HOH B:1106 , HOH B:1168 , HOH B:1421 , HOH B:1456 , HOH B:1510
BINDING SITE FOR RESIDUE PO4 B 880
08
AC8
SOFTWARE
GLY A:39 , GLY A:40 , LYS A:66 , LYS A:78 , PRO A:117 , ASP A:118 , ASN A:262 , ALA A:292 , LEU A:295 , NAI A:360 , HOH A:1046 , HOH A:1226
BINDING SITE FOR RESIDUE PHE A 361
09
AC9
SOFTWARE
GLY B:39 , GLY B:40 , MET B:63 , LYS B:66 , LYS B:78 , PRO B:117 , ASP B:118 , ASN B:262 , NAI B:760 , HOH B:1008 , HOH B:1073
BINDING SITE FOR RESIDUE PHE B 761
10
BC1
SOFTWARE
ARG A:42 , ASP A:118 , SER A:149 , THR A:153 , GLY A:182 , LEU A:183 , GLY A:184 , ALA A:185 , VAL A:186 , ASP A:205 , THR A:206 , LEU A:224 , CYS A:238 , ALA A:239 , ALA A:260 , ALA A:261 , ASN A:262 , ASN A:288 , PHE A:361 , HOH A:1082 , HOH A:1149 , HOH A:1163 , HOH A:1281 , HOH A:1488 , HOH A:1493 , HOH A:1786 , HOH A:1867
BINDING SITE FOR RESIDUE NAI A 360
11
BC2
SOFTWARE
ARG B:42 , ASP B:118 , SER B:149 , THR B:153 , GLY B:182 , LEU B:183 , GLY B:184 , ALA B:185 , VAL B:186 , ASP B:205 , THR B:206 , ARG B:210 , CYS B:238 , ALA B:239 , MET B:240 , ALA B:260 , ALA B:261 , ASN B:262 , ASN B:288 , PHE B:761 , HOH B:1091 , HOH B:1123 , HOH B:1300 , HOH B:1320 , HOH B:1498
BINDING SITE FOR RESIDUE NAI B 760
12
BC3
SOFTWARE
THR A:15 , ARG B:28 , HOH B:1062
BINDING SITE FOR RESIDUE IPA B 860
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1c1da2 (A:1-148)
1b: SCOP_d1c1db2 (B:1-148)
2a: SCOP_d1c1da1 (A:149-349)
2b: SCOP_d1c1db1 (B:149-348)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Aminoacid dehydrogenases
(28)
Protein domain
:
Phenylalanine dehydrogenase
(4)
Rhodococcus sp., M4 [TaxId: 1831]
(4)
1a
d1c1da2
A:1-148
1b
d1c1db2
B:1-148
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Phenylalanine dehydrogenase
(4)
Rhodococcus sp., M4 [TaxId: 1831]
(4)
2a
d1c1da1
A:149-349
2b
d1c1db1
B:149-348
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1c1dA01 (A:3-64,A:75-136,A:339-349)
1b: CATH_1c1dB01 (B:3-64,B:75-136,B:339-348)
2a: CATH_1c1dA02 (A:137-338)
2b: CATH_1c1dB02 (B:137-338)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Leucine Dehydrogenase; Chain A, domain 1
(52)
Homologous Superfamily
:
Leucine Dehydrogenase, chain A, domain 1
(52)
Rhodococcus sp.. Organism_taxid: 1831.
(2)
1a
1c1dA01
A:3-64,A:75-136,A:339-349
1b
1c1dB01
B:3-64,B:75-136,B:339-348
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodococcus sp.. Organism_taxid: 1831.
(2)
2a
1c1dA02
A:137-338
2b
1c1dB02
B:137-338
[
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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (125 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
1C1D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help