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.
1D1Y
Asym. Unit
Info
Asym.Unit (152 KB)
Biol.Unit 1 (145 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 1, 3-PBITU (H4B FREE)
Authors
:
C. S. Raman, H. Li, P. Martasek, G. J. Southan, B. S. S. Masters, T. L. Poul
Date
:
21 Sep 99 (Deposition) - 25 Jul 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Alpha-Beta Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. S. Raman, H. Li, P. Martasek, B. R. Babu, O. W. Griffith, B. S. Masters T. L. Poulos
Implications For Isoform-Selective Inhibitor Design Derived From The Binding Mode Of Bulky Isothioureas To The Heme Domain Of Endothelial Nitric-Oxide Synthase.
J. Biol. Chem. V. 276 26486 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 16)
Info
All Hetero Components
1a: 2-{2-[3-(2-CARBAMIMIDOYLSULFANYL-E... (3BTa)
1b: 2-{2-[3-(2-CARBAMIMIDOYLSULFANYL-E... (3BTb)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
3a: CACODYLIC ACID (CADa)
3b: CACODYLIC ACID (CADb)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
7a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3BT
2
Ligand/Ion
2-{2-[3-(2-CARBAMIMIDOYLSULFANYL-ETHYL)-PHENYL]-ETHYL}-ISOTHIOUREA
2
ACT
4
Ligand/Ion
ACETATE ION
3
CAD
2
Ligand/Ion
CACODYLIC ACID
4
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
5
GOL
3
Ligand/Ion
GLYCEROL
6
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
ZN
1
Ligand/Ion
ZINC ION
[
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
GLN A:249 , ARG A:252 , ASN A:368 , ARG A:374 , HOH A:1027
BINDING SITE FOR RESIDUE ACT A 850
02
AC2
SOFTWARE
GLY A:188 , TRP A:358 , VAL A:420 , SER A:428 , HOH A:1107
BINDING SITE FOR RESIDUE ACT A 860
03
AC3
SOFTWARE
GLN B:249 , ARG B:252 , ASN B:368 , ARG B:374 , HOH B:975
BINDING SITE FOR RESIDUE ACT B 851
04
AC4
SOFTWARE
GLY B:188 , TRP B:358 , VAL B:420 , SER B:428 , HOH B:1030
BINDING SITE FOR RESIDUE ACT B 861
05
AC5
SOFTWARE
CYS A:96 , CYS A:101 , CYS B:96 , CYS B:101
BINDING SITE FOR RESIDUE ZN B 900
06
AC6
SOFTWARE
TRP A:180 , ARG A:185 , CYS A:186 , SER A:228 , MET A:341 , PHE A:355 , SER A:356 , TRP A:358 , GLU A:363 , TRP A:449 , TYR A:477 , 3BT A:820 , GOL A:890 , HOH A:1064 , HOH A:1074 , HOH A:1119
BINDING SITE FOR RESIDUE HEM A 500
07
AC7
SOFTWARE
TRP B:180 , ARG B:185 , CYS B:186 , SER B:228 , PHE B:355 , SER B:356 , TRP B:358 , GLU B:363 , TRP B:449 , TYR B:477 , 3BT B:821 , GOL B:891 , HOH B:956 , HOH B:986 , HOH B:1060
BINDING SITE FOR RESIDUE HEM B 500
08
AC8
SOFTWARE
SER A:248 , GLN A:249 , PRO A:336 , VAL A:338 , PHE A:355 , TRP A:358 , TYR A:359 , GLU A:363 , HEM A:500 , HOH A:970
BINDING SITE FOR RESIDUE 3BT A 820
09
AC9
SOFTWARE
ARG A:367 , HIS A:373 , GOL A:890 , HOH A:979 , TRP B:76 , HOH B:1038
BINDING SITE FOR RESIDUE EDO A 870
10
BC1
SOFTWARE
TRP A:324 , CYS A:384 , LYS A:438 , ARG A:440 , GLY A:441
BINDING SITE FOR RESIDUE CAD A 950
11
BC2
SOFTWARE
GLN B:249 , PRO B:336 , VAL B:338 , ASN B:340 , TRP B:358 , TYR B:359 , GLU B:363 , HEM B:500
BINDING SITE FOR RESIDUE 3BT B 821
12
BC3
SOFTWARE
ARG B:367 , HIS B:373 , GOL B:891 , HOH B:994
BINDING SITE FOR RESIDUE EDO B 871
13
BC4
SOFTWARE
PHE B:70 , TYR B:83 , TRP B:324 , CYS B:384
BINDING SITE FOR RESIDUE CAD B 951
14
BC5
SOFTWARE
ARG A:367 , TRP A:449 , HEM A:500 , EDO A:870 , HOH A:962 , PHE B:462
BINDING SITE FOR RESIDUE GOL A 890
15
BC6
SOFTWARE
PHE A:462 , GLU A:465 , SER B:104 , TRP B:449 , GOL B:891
BINDING SITE FOR RESIDUE GOL A 881
16
BC7
SOFTWARE
GOL A:881 , ARG B:367 , ALA B:448 , TRP B:449 , HEM B:500 , EDO B:871
BINDING SITE FOR RESIDUE GOL B 891
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: NOS (A:185-192,B:185-192)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NOS
PS60001
Nitric oxide synthase (NOS) signature.
NOS3_BOVIN
185-192
2
A:185-192
B:185-192
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d1d1ya_ (A:)
1b: SCOP_d1d1yb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nitric oxide (NO) synthase oxygenase domain
(313)
Superfamily
:
Nitric oxide (NO) synthase oxygenase domain
(313)
Family
:
Nitric oxide (NO) synthase oxygenase domain
(313)
Protein domain
:
Nitric oxide (NO) synthase oxygenase domain
(298)
Cow (Bos taurus) [TaxId: 9913]
(85)
1a
d1d1ya_
A:
1b
d1d1yb_
B:
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1d1yA03 (A:314-336,A:359-424)
1b: CATH_1d1yB03 (B:314-336,B:359-424)
2a: CATH_1d1yA01 (A:84-201,A:228-238,A:342-356,A:426-450)
2b: CATH_1d1yB01 (B:84-201,B:228-238,B:342-356,B:426-450)
3a: CATH_1d1yA02 (A:202-227,A:242-313,A:477-481)
3b: CATH_1d1yB02 (B:202-227,B:242-313,B:477-481)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
(105)
Homologous Superfamily
:
Nitric Oxide Synthase; Chain A, domain 3
(105)
Cattle (Bos taurus)
(38)
1a
1d1yA03
A:314-336,A:359-424
1b
1d1yB03
B:314-336,B:359-424
Topology
:
Nitric Oxide Synthase; Chain A, domain 1
(105)
Homologous Superfamily
:
Nitric Oxide Synthase; Chain A, domain 1
(105)
Cattle (Bos taurus)
(38)
2a
1d1yA01
A:84-201,A:228-238,A:342-356,A:426-450
2b
1d1yB01
B:84-201,B:228-238,B:342-356,B:426-450
Topology
:
Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
(105)
Homologous Superfamily
:
Nitric Oxide Synthase;Heme Domain;Chain A domain 2
(105)
Cattle (Bos taurus)
(38)
3a
1d1yA02
A:202-227,A:242-313,A:477-481
3b
1d1yB02
B:202-227,B:242-313,B:477-481
[
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 (152 KB)
Header - Asym.Unit
Biol.Unit 1 (145 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
1D1Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
