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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2CF7
Asym. Unit
Info
Asym.Unit (350 KB)
Biol.Unit 1 (342 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ASP74ALA MUTANT CRYSTAL STRUCTURE FOR DPS-LIKE PEROXIDE RESISTANCE PROTEIN DPR FROM STREPTOCOCCUS SUIS.
Authors
:
A. Kauko, A. T. Pulliainen, S. Haataja, J. Finne, A. C. Papageorgiou
Date
:
16 Feb 06 (Deposition) - 28 Sep 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Peroxide Resistance, Dps-Family, Ferritin-Like, Ferroxidase, Iron-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kauko, A. T. Pulliainen, S. Haataja, W. Meyer-Klaucke, J. Finne, A. C. Papageorgiou
Iron Incorporation In Streptococcus Suis Dps-Like Peroxide Resistance Protein Dpr Requires Mobility In The Ferroxidase Center And Leads To The Formation Of A Ferrihydrite-Like Core.
J. Mol. Biol. V. 364 97 2006
[
close entry info
]
Hetero Components
(3, 9)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEb)
3c: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEc)
3d: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
[
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
HOH C:2071 , HOH C:2072 , HOH C:2153 , HOH H:2067 , HOH H:2162 , HOH H:2163 , HOH J:2155
BINDING SITE FOR RESIDUE CA D3173
2
AC2
SOFTWARE
ILE J:111 , HOH J:2042
BINDING SITE FOR RESIDUE CL J3173
3
AC3
SOFTWARE
HOH B:2079 , HOH B:2165 , HOH J:2037 , HOH J:2116 , HOH J:2119 , HOH J:2120 , HOH K:2169
BINDING SITE FOR RESIDUE CA J3174
4
AC4
SOFTWARE
HOH B:2176 , ILE K:111
BINDING SITE FOR RESIDUE CL K3174
5
AC5
SOFTWARE
HOH A:2083 , HOH A:2164 , HOH J:2169 , HOH K:2027 , HOH K:2114 , HOH K:2115 , HOH K:2118
BINDING SITE FOR RESIDUE CA K3175
6
AC6
SOFTWARE
GLU A:112 , ARG B:53 , GLY B:54 , ILE B:57 , HOH B:2173 , HOH B:2174 , HOH B:2175 , HOH B:2176 , HOH B:2177 , HOH B:2178 , HOH B:2179 , ARG F:53 , GLY F:54 , ILE F:57 , HOH F:2173 , ARG J:53 , GLY J:54 , ILE J:57 , ARG K:53 , EPE K:3173
BINDING SITE FOR RESIDUE EPE B3173
7
AC7
SOFTWARE
GLY C:54 , HOH C:2163 , ARG E:53 , GLY E:54 , HOH E:2045 , HOH E:2149 , HOH E:2150 , HOH E:2151 , HOH E:2152 , HOH E:2153 , ASP H:137 , GLU H:138 , ARG L:53 , GLY L:54 , ILE L:57 , HOH L:2135
BINDING SITE FOR RESIDUE EPE E3173
8
AC8
SOFTWARE
ARG D:53 , GLY D:54 , HOH D:2173 , ASP F:137 , GLU F:138 , GLY G:54 , ILE G:57 , HOH G:2139 , HOH G:2153 , GLY I:54 , ILE I:57 , HOH I:2160
BINDING SITE FOR RESIDUE EPE G3173
9
AC9
SOFTWARE
ARG A:53 , GLY A:54 , EPE B:3173 , ARG H:53 , GLY H:54 , ILE H:57 , ARG K:53 , GLY K:54 , ILE K:57 , HOH K:2181 , HOH K:2182 , HOH K:2183 , HOH K:2184 , HOH K:2185 , HOH K:2186 , HOH K:2187
BINDING SITE FOR RESIDUE EPE K3173
[
close Site info
]
SAPs(SNPs)/Variants
(9, 108)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DPS_STRSU_001 (A27S, chain A/B/C/D/E/F/G/H/I/J/K/L, )
2: VAR_DPS_STRSU_002 (I42L, chain A/B/C/D/E/F/G/H/I/J/K/L, )
3: VAR_DPS_STRSU_003 (L91F, chain A/B/C/D/E/F/G/H/I/J/K/L, )
4: VAR_DPS_STRSU_004 (V103A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
5: VAR_DPS_STRSU_005 (L104P, chain A/B/C/D/E/F/G/H/I/J/K/L, )
6: VAR_DPS_STRSU_006 (T110M, chain A/B/C/D/E/F/G/H/I/J/K/L, )
7: VAR_DPS_STRSU_007 (A116V, chain A/B/C/D/E/F/G/H/I/J/K/L, )
8: VAR_DPS_STRSU_008 (S154N, chain A/B/C/D/E/F/G/H/I/J/K/L, )
9: VAR_DPS_STRSU_009 (K171G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DPS_STRSU_001
*
A
27
S
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
27
S
2
UniProt
VAR_DPS_STRSU_002
*
I
42
L
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
I
42
L
3
UniProt
VAR_DPS_STRSU_003
*
L
91
F
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
91
F
4
UniProt
VAR_DPS_STRSU_004
*
V
103
A
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
V
103
A
5
UniProt
VAR_DPS_STRSU_005
*
L
104
P
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
104
P
6
UniProt
VAR_DPS_STRSU_006
*
T
110
M
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
T
110
M
7
UniProt
VAR_DPS_STRSU_007
*
A
116
V
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
116
V
8
UniProt
VAR_DPS_STRSU_008
*
S
154
N
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
S
154
N
9
UniProt
VAR_DPS_STRSU_009
*
K
171
G
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
171
G
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d2cf7a_ (A:)
1b: SCOP_d2cf7b_ (B:)
1c: SCOP_d2cf7k_ (K:)
1d: SCOP_d2cf7l_ (L:)
1e: SCOP_d2cf7c_ (C:)
1f: SCOP_d2cf7d_ (D:)
1g: SCOP_d2cf7e_ (E:)
1h: SCOP_d2cf7f_ (F:)
1i: SCOP_d2cf7g_ (G:)
1j: SCOP_d2cf7h_ (H:)
1k: SCOP_d2cf7i_ (I:)
1l: SCOP_d2cf7j_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
automated matches
(70)
Streptococcus suis [TaxId: 1307]
(1)
1a
d2cf7a_
A:
1b
d2cf7b_
B:
1c
d2cf7k_
K:
1d
d2cf7l_
L:
1e
d2cf7c_
C:
1f
d2cf7d_
D:
1g
d2cf7e_
E:
1h
d2cf7f_
F:
1i
d2cf7g_
G:
1j
d2cf7h_
H:
1k
d2cf7i_
I:
1l
d2cf7j_
J:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2cf7A00 (A:14-172)
1b: CATH_2cf7G00 (G:20-172)
1c: CATH_2cf7L00 (L:22-172)
1d: CATH_2cf7B00 (B:23-172)
1e: CATH_2cf7C00 (C:21-172)
1f: CATH_2cf7D00 (D:21-172)
1g: CATH_2cf7I00 (I:21-172)
1h: CATH_2cf7E00 (E:22-172)
1i: CATH_2cf7F00 (F:22-172)
1j: CATH_2cf7H00 (H:22-172)
1k: CATH_2cf7J00 (J:22-172)
1l: CATH_2cf7K00 (K:22-172)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Streptococcus suis. Organism_taxid: 1307. Strain: d282.
(5)
1a
2cf7A00
A:14-172
1b
2cf7G00
G:20-172
1c
2cf7L00
L:22-172
1d
2cf7B00
B:23-172
1e
2cf7C00
C:21-172
1f
2cf7D00
D:21-172
1g
2cf7I00
I:21-172
1h
2cf7E00
E:22-172
1i
2cf7F00
F:22-172
1j
2cf7H00
H:22-172
1k
2cf7J00
J:22-172
1l
2cf7K00
K:22-172
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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 (350 KB)
Header - Asym.Unit
Biol.Unit 1 (342 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
2CF7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help