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.
2QFN
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (114 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTAL STRUCTURE ANALYSIS OF THE BINDING SITE IN THE FERRIC AND OXYFERROUS FORMS OF THE RECOMBINANT HEME DEHALOPEROXIDASE CLONED FROM AMPHITRITE ORNATA
Authors
:
V. De Serrano, Z. Chen, M. F. Davis, S. Franzen
Date
:
27 Jun 07 (Deposition) - 20 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.62
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dehaloperoxidase, Dhp, Globin, Heme Protein, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. De Serrano, Z. Chen, M. F. Davis, S. Franzen
X-Ray Crystal Structural Analysis Of The Binding Site In The Ferric And Oxyferrous Forms Of The Recombinant Heme Dehaloperoxidase Cloned From Amphitrite Ornata
Acta Crystallogr. , Sect. D V. 63 1094 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2a: AMMONIUM ION (NH4a)
2b: AMMONIUM ION (NH4b)
3a: OXYGEN MOLECULE (OXYa)
3b: OXYGEN MOLECULE (OXYb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NH4
2
Ligand/Ion
AMMONIUM ION
3
OXY
2
Ligand/Ion
OXYGEN MOLECULE
4
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:19 , LEU A:22 , LYS A:47
BINDING SITE FOR RESIDUE NH4 A 192
2
AC2
SOFTWARE
GLY A:1 , PHE A:2 , LYS A:3 , HOH A:256 , HOH A:281 , HOH A:309 , ARG B:32 , GLY B:40
BINDING SITE FOR RESIDUE SO4 B 195
3
AC3
SOFTWARE
LYS A:99 , HOH A:198 , HOH A:330 , GLU B:31 , ARG B:33 , TYR B:34 , ASN B:96 , LYS B:99 , HOH B:274 , HOH B:275
BINDING SITE FOR RESIDUE SO4 B 196
4
AC4
SOFTWARE
ARG A:32 , GLY A:40 , HOH A:210 , HOH A:239 , HOH A:241 , GLY B:1 , PHE B:2 , LYS B:3 , ASP B:116 , HOH B:215
BINDING SITE FOR RESIDUE SO4 A 197
5
AC5
SOFTWARE
ASP B:19 , TYR B:107
BINDING SITE FOR RESIDUE NH4 B 191
6
AC6
SOFTWARE
PHE A:24 , GLU A:31 , TYR A:34 , PHE A:35 , ASP A:54 , HIS A:55 , LYS A:58 , MET A:86 , GLN A:88 , HIS A:89 , LEU A:92 , ASN A:96 , PHE A:97 , HOH A:204 , HOH A:232 , HOH A:310 , HOH A:316 , HOH A:338
BINDING SITE FOR RESIDUE HEM A 139
7
AC7
SOFTWARE
GLU B:31 , TYR B:34 , PHE B:35 , HIS B:55 , LYS B:58 , MET B:63 , MET B:86 , GLN B:88 , HIS B:89 , LEU B:92 , ASN B:96 , PHE B:97 , LEU B:127
BINDING SITE FOR RESIDUE HEM B 139
8
AC8
SOFTWARE
PHE A:21 , HIS A:55
BINDING SITE FOR RESIDUE OXY A 186
9
AC9
SOFTWARE
HIS B:55
BINDING SITE FOR RESIDUE OXY B 187
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2qfna_ (A:)
1b: SCOP_d2qfnb_ (B:)
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
:
Dehaloperoxidase
(30)
Amphitrite ornata [TaxId: 129555]
(30)
1a
d2qfna_
A:
1b
d2qfnb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2qfnA00 (A:1-137)
1b: CATH_2qfnB00 (B:1-137)
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)
Amphitrite oRNAta.
(2)
1a
2qfnA00
A:1-137
1b
2qfnB00
B:1-137
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Globin_2qfnB01 (B:2-128)
1b: PFAM_Globin_2qfnB02 (B:2-128)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Globin
(291)
Family
:
Globin
(264)
Amphitrite ornata
(12)
1a
Globin-2qfnB01
B:2-128
1b
Globin-2qfnB02
B:2-128
[
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 (119 KB)
Header - Asym.Unit
Biol.Unit 1 (114 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
2QFN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
