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.
3QZX
Asym. Unit
Info
Asym.Unit (86 KB)
Biol.Unit 1 (159 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
3D STRUCTURE OF FERRIC METHANOSARCINA ACETIVORANS PROTOGLOBIN Y61A MUTANT WITH UNKNOWN LIGAND
Authors
:
A. Pesce, L. Tilleman, S. Dewilde, P. Ascenzi, M. Coletta, C. Ciaccio, S L. Moens, M. Bolognesi, M. Nardini
Date
:
07 Mar 11 (Deposition) - 08 Jun 11 (Release) - 08 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Globin Fold, Protoglobin, Methanogenesis, Archaea Protein, Oxygen Binding, Oxygen Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Pesce, L. Tilleman, S. Dewilde, P. Ascenzi, M. Coletta, C. Ciaccio, S. Bruno, L. Moens, M. Bolognesi, M. Nardini
Structural Heterogeneity And Ligand Gating In Ferric Methanosarcina Acetivorans Protoglobin Mutants.
Iubmb Life V. 63 287 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:70 , TYR A:73 , PHE A:74 , TYR A:85 , VAL A:89 , ARG A:92 , PHE A:93 , TRP A:96 , TYR A:112 , ARG A:119 , HIS A:120 , LYS A:125 , ASN A:126 , ILE A:137 , TYR A:141 , LEU A:142 , PHE A:145 , ILE A:149 , VAL A:182 , TRP A:185 , HOH A:269 , HOH A:279 , HOH A:281 , HOH A:282
BINDING SITE FOR RESIDUE HEM A 200
2
AC2
SOFTWARE
GLY A:12 , GLU A:13 , THR A:14 , GLU A:15 , ASN A:16 , ALA A:108 , ASP A:111 , HOH A:259
BINDING SITE FOR RESIDUE PO4 A 201
3
AC3
SOFTWARE
TYR A:72 , VAL A:134 , PRO A:135 , ASN A:136 , HOH A:219 , HOH A:234 , HOH A:271 , HOH A:289 , HOH A:387
BINDING SITE FOR RESIDUE PO4 A 202
4
AC4
SOFTWARE
THR A:163 , PRO A:164 , GLU A:165 , TYR A:187 , PRO A:188 , VAL A:190 , LYS A:191 , TYR A:192 , HOH A:365 , HOH A:427
BINDING SITE FOR RESIDUE GOL A 204
[
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
(1, 1)
Info
all PFAM domains
1a: PFAM_Protoglobin_3qzxA01 (A:6-195)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Protoglobin]
(5)
Family
:
Protoglobin
(5)
Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
(5)
1a
Protoglobin-3qzxA01
A:6-195
[
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
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 (86 KB)
Header - Asym.Unit
Biol.Unit 1 (159 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
3QZX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
