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.
2R50
Asym. Unit
Info
Asym.Unit (117 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (109 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF NONSYMBIOTIC CORN HEMOGLOBIN 1
Authors
:
B. J. Smagghe, J. A. Hoy, M. S. Hargrove
Date
:
02 Sep 07 (Deposition) - 18 Sep 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Corn Hemoglobin, Plant Hemoglobin, Nonsymbiotic Hemoglobin, Heme, Iron, Metal-Binding, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Smagghe, J. A. Hoy, M. S. Hargrove
The Crystal Structure Of Nonsymbiotic Corn Hemoglobin 1
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
2
Ligand/Ion
ACETIC ACID
2
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:110 , TYR B:111 , HOH B:204 , HOH B:205 , PRO C:163 , ASP C:164 , HOH C:195
BINDING SITE FOR RESIDUE SO4 B 166
02
AC2
SOFTWARE
ASP B:164 , HOH B:304 , ARG C:110 , TYR C:111
BINDING SITE FOR RESIDUE SO4 C 166
03
AC3
SOFTWARE
LYS C:130 , TRP C:138 , LYS C:143 , HOH C:276 , HOH C:281
BINDING SITE FOR RESIDUE SO4 C 167
04
AC4
SOFTWARE
ARG A:110 , TYR A:111 , LYS D:162 , PRO D:163 , ASP D:164
BINDING SITE FOR RESIDUE SO4 D 166
05
AC5
SOFTWARE
ASP A:164 , ARG D:110 , TYR D:111 , HOH D:230
BINDING SITE FOR RESIDUE SO4 D 167
06
AC6
SOFTWARE
MET A:53 , PHE A:54 , LYS A:69 , HIS A:73 , ARG A:103 , LEU A:104 , THR A:107 , HIS A:108 , TYR A:111 , HIS A:117 , THR A:121 , ILE A:157 , HOH A:212 , HOH A:326
BINDING SITE FOR RESIDUE HEM A 166
07
AC7
SOFTWARE
MET B:53 , PHE B:54 , LYS B:69 , HIS B:73 , ARG B:103 , LEU B:104 , HIS B:108 , TYR B:111 , HIS B:117 , THR B:121 , HOH B:191 , HOH B:283
BINDING SITE FOR RESIDUE HEM B 167
08
AC8
SOFTWARE
MET C:53 , PHE C:56 , HIS C:73 , ARG C:103 , LEU C:104 , THR C:107 , HIS C:108 , TYR C:111 , HIS C:117 , THR C:121 , LEU C:153 , HOH C:224
BINDING SITE FOR RESIDUE HEM C 168
09
AC9
SOFTWARE
LYS D:69 , HIS D:73 , MET D:80 , ARG D:103 , LEU D:104 , THR D:107 , HIS D:108 , TYR D:111 , VAL D:113 , HIS D:117 , THR D:121
BINDING SITE FOR RESIDUE HEM D 168
10
BC1
SOFTWARE
PHE B:39 , PHE B:40 , HIS B:73 , ALA B:74 , VAL B:77 , HOH B:176
BINDING SITE FOR RESIDUE ACY B 168
11
BC2
SOFTWARE
PHE D:40 , HIS D:73 , ALA D:74 , VAL D:77 , HOH D:173
BINDING SITE FOR RESIDUE ACY D 169
[
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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GLOBIN (A:13-162,B:13-162,C:13-162,D:13-16...)
2: PLANT_GLOBIN (A:67-78,B:67-78,C:67-78,D:67-78)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLOBIN
PS01033
Globin family profile.
HBL_ZEAMP
13-162
4
A:13-162
B:13-162
C:13-162
D:13-162
2
PLANT_GLOBIN
PS00208
Plant hemoglobins signature.
HBL_ZEAMP
67-78
4
A:67-78
B:67-78
C:67-78
D:67-78
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d2r50a_ (A:)
1b: SCOP_d2r50b_ (B:)
1c: SCOP_d2r50c_ (C:)
1d: SCOP_d2r50d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
Globin-like
(1308)
Family
:
Globins
(1157)
Protein domain
:
automated matches
(99)
Maize (Zea mays) [TaxId: 76912]
(1)
1a
d2r50a_
A:
1b
d2r50b_
B:
1c
d2r50c_
C:
1d
d2r50d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2r50D00 (D:12-165)
1b: CATH_2r50A00 (A:11-165)
1c: CATH_2r50B00 (B:11-165)
1d: CATH_2r50C00 (C:12-165)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Globin-like
(786)
Homologous Superfamily
:
Globins
(743)
Parviglumis (Zea mays subsp)
(1)
1a
2r50D00
D:12-165
1b
2r50A00
A:11-165
1c
2r50B00
B:11-165
1d
2r50C00
C:12-165
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Globin_2r50D01 (D:17-126)
1b: PFAM_Globin_2r50D02 (D:17-126)
1c: PFAM_Globin_2r50D03 (D:17-126)
1d: PFAM_Globin_2r50D04 (D:17-126)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Globin
(291)
Family
:
Globin
(264)
Zea mays subsp. parviglumis (Balsas teosinte)
(1)
1a
Globin-2r50D01
D:17-126
1b
Globin-2r50D02
D:17-126
1c
Globin-2r50D03
D:17-126
1d
Globin-2r50D04
D:17-126
[
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 (117 KB)
Header - Asym.Unit
Biol.Unit 1 (55 KB)
Header - Biol.Unit 1
Biol.Unit 2 (57 KB)
Header - Biol.Unit 2
Biol.Unit 3 (109 KB)
Header - Biol.Unit 3
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
2R50
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help