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.
5E29
Asym. Unit
Info
Asym.Unit (121 KB)
Biol.Unit 1 (115 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 DEOXYGENATED HEMOGLOBIN IN COMPLEX WITH AN ALLOSTERIC EFFECTOR AND NITRIC OXIDE
Authors
:
M. K. Safo, T. M. Deshpande
Date
:
30 Sep 15 (Deposition) - 14 Oct 15 (Release) - 30 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hemoglobin, Right-Shifter, Nitric Oxide, Oxygen Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. G. Xu, T. M. Deshpande, M. S. Ghatge, A. Y. Mehta, A. S. Omar, M. H. Ahmed, J. Venitz, O. Abdulmalik, Y. Zhang, M. K. Safo
Design, Synthesis, And Investigation Of Novel Nitric Oxide (No)-Releasing Prodrugs As Drug Candidates For The Treatmen Of Ischemic Disorders: Insights Into No-Releasing Prodrug Biotransformation And Hemoglobin-No Biochemistry.
Biochemistry V. 54 7178 2015
[
close entry info
]
Hetero Components
(6, 12)
Info
All Hetero Components
1a: 2-(NITROOXY)ETHYL 2-(4-{2-[(3,5-DI... (5JNa)
2a: CACODYLATE ION (CACa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4a: NITRATE ION (NO3a)
4b: NITRATE ION (NO3b)
5a: NITRIC OXIDE (NOa)
5b: NITRIC OXIDE (NOb)
6a: 2-{4-[(3,5-DIMETHYLANILINO)-CARBON... (RQ3a)
6b: 2-{4-[(3,5-DIMETHYLANILINO)-CARBON... (RQ3b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5JN
1
Ligand/Ion
2-(NITROOXY)ETHYL 2-(4-{2-[(3,5-DIMETHYLPHENYL)AMINO]-2-OXOETHYL}PHENOXY)-2-METHYLPROPANOATE
2
CAC
1
Ligand/Ion
CACODYLATE ION
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
NO
2
Ligand/Ion
NITRIC OXIDE
4
NO3
2
Ligand/Ion
NITRATE ION
6
RQ3
2
Ligand/Ion
2-{4-[(3,5-DIMETHYLANILINO)-CARBONYL-METHYL]-PHENOXY}-2-METHYLPROPIONIC ACID
[
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:58 , VAL A:62 , HEM A:202
binding site for residue NO A 201
02
AC2
SOFTWARE
TYR A:42 , PHE A:43 , HIS A:45 , PHE A:46 , HIS A:58 , LYS A:61 , LEU A:86 , HIS A:87 , LEU A:91 , VAL A:93 , ASN A:97 , PHE A:98 , LEU A:101 , LEU A:136 , NO A:201 , HOH A:305 , HOH A:364 , LYS D:17
binding site for residue HEM A 202
03
AC3
SOFTWARE
LYS A:99 , LEU A:100 , HIS A:103 , ALA A:130 , SER A:131 , THR A:134 , HOH A:332 , HOH A:386 , HOH A:393 , HOH A:414 , TYR B:35 , TRP B:37 , ASN B:108 , RQ3 B:202 , HOH B:424 , PRO C:95 , THR C:137 , TYR C:140 , ARG C:141 , HOH C:396
binding site for residue 5JN A 203
04
AC4
SOFTWARE
PRO A:95 , THR A:137 , ARG A:141 , HOH A:362 , HOH A:385 , PHE C:36 , LYS C:99 , LEU C:100 , HIS C:103 , HOH C:365 , TYR D:35 , TRP D:37 , ASN D:108 , HOH D:466
binding site for residue RQ3 A 204
05
AC5
SOFTWARE
LYS A:56 , PHE B:41 , PHE B:45 , HIS B:63 , LYS B:66 , VAL B:67 , ALA B:70 , LEU B:91 , HIS B:92 , LEU B:96 , ASN B:102 , PHE B:103 , LEU B:106 , LEU B:141 , HOH B:312 , HOH B:379
binding site for residue HEM B 201
06
AC6
SOFTWARE
LYS A:99 , LEU A:100 , HIS A:103 , 5JN A:203 , HOH A:307 , HOH A:356 , HOH A:386 , TYR B:35 , TRP B:37 , ASN B:108 , PRO C:95 , THR C:137 , ARG C:141
binding site for residue RQ3 B 202
07
AC7
SOFTWARE
LYS B:95 , HIS B:97 , HOH B:364 , HOH B:381 , HOH B:385 , HOH B:396 , HOH B:398 , HIS C:45
binding site for residue NO3 B 203
08
AC8
SOFTWARE
HIS C:58 , VAL C:62 , HEM C:202
binding site for residue NO C 201
09
AC9
SOFTWARE
TYR C:42 , PHE C:43 , PHE C:46 , HIS C:58 , LYS C:61 , LEU C:83 , LEU C:86 , HIS C:87 , LEU C:91 , VAL C:93 , ASN C:97 , PHE C:98 , LEU C:101 , NO C:201 , HOH C:301 , HOH C:302 , HOH C:322 , HOH C:328 , HOH C:368 , HOH C:398
binding site for residue HEM C 202
10
AD1
SOFTWARE
HIS C:72 , ASP C:75 , HOH C:327 , PHE D:41 , HIS D:63 , LYS D:66 , VAL D:67 , LEU D:88 , LEU D:91 , HIS D:92 , LEU D:96 , ASN D:102 , PHE D:103 , LEU D:141 , HOH D:323 , HOH D:333 , HOH D:382 , HOH D:383 , HOH D:390 , HOH D:406 , HOH D:426
binding site for residue HEM D 201
11
AD2
SOFTWARE
HOH D:310 , HOH D:312 , HOH D:318 , HOH D:327 , HOH D:332 , HOH D:334 , HOH D:342 , HOH D:378 , HOH D:384 , HOH D:391 , HOH D:468
binding site for residue CAC D 202
12
AD3
SOFTWARE
ASP D:94 , LYS D:95 , HIS D:97 , HOH D:307 , HOH D:338 , HOH D:408
binding site for residue NO3 D 203
[
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
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 (121 KB)
Header - Asym.Unit
Biol.Unit 1 (115 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
5E29
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help