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.
1UMN
Asym. Unit
Info
Asym.Unit (336 KB)
Biol.Unit 1 (328 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 DPS-LIKE PEROXIDE RESISTANCE PROTEIN (DPR) FROM STREPTOCOCCUS SUIS
Authors
:
A. Kauko, S. Haataja, A. Pulliainen, J. Finne, A. C. Papageorgiou
Date
:
26 Aug 03 (Deposition) - 23 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
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, Iron-Binding, Ferroxidase, Dps-Family, Ferritin-Like
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kauko, S. Haataja, A. Pulliainen, J. Finne, A. C. Papageorgiou
Crystal Structure Of Streptococcus Suis Dps-Like Peroxide Resistance Protein Dpr: Implications For Iron Incorporation
J. Mol. Biol. V. 338 547 2004
[
close entry info
]
Hetero Components
(3, 23)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
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
16
Ligand/Ion
CALCIUM ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
[
close Hetero Component info
]
Sites
(23, 23)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:63 , HOH A:2043 , HOH A:2044 , HOH C:2052 , HOH C:2053
BINDING SITE FOR RESIDUE CA A2173
02
AC2
SOFTWARE
ASP B:63 , HOH B:2043 , HOH B:2045 , HOH D:2064 , HOH D:2073 , HOH D:2074
BINDING SITE FOR RESIDUE CA B2173
03
AC3
SOFTWARE
HOH A:2024 , HOH A:2061 , HOH A:2063 , ASP C:63 , HOH C:2037 , HOH C:2038
BINDING SITE FOR RESIDUE CA C2173
04
AC4
SOFTWARE
HOH A:2115 , ILE D:111 , HOH D:2037
BINDING SITE FOR RESIDUE CL D1174
05
AC5
SOFTWARE
HOH A:2111 , HOH A:2147 , HOH D:2032 , HOH D:2112 , HOH D:2114 , HOH D:2116 , HOH G:2129
BINDING SITE FOR RESIDUE CA D1175
06
AC6
SOFTWARE
HOH B:2024 , HOH B:2064 , HOH B:2065 , ASP D:63 , HOH D:2049 , HOH D:2051
BINDING SITE FOR RESIDUE CA D2173
07
AC7
SOFTWARE
ASP E:63 , HOH E:2020 , HOH E:2046 , HOH G:2056 , HOH G:2058
BINDING SITE FOR RESIDUE CA E2173
08
AC8
SOFTWARE
ASP F:63 , HOH F:2027 , HOH F:2048 , HOH H:2044 , HOH H:2045
BINDING SITE FOR RESIDUE CA F2173
09
AC9
SOFTWARE
ASN G:108 , HOH G:2086 , HOH G:2097 , ASN H:108 , HOH H:2082 , HOH H:2084 , HOH K:2140
BINDING SITE FOR RESIDUE CA G1174
10
BC1
SOFTWARE
HOH E:2025 , HOH E:2059 , HOH E:2060 , ASP G:63 , HOH G:2042 , HOH G:2044
BINDING SITE FOR RESIDUE CA G2173
11
BC2
SOFTWARE
GLY H:52 , ILE H:111 , HOH H:2020 , HOH H:2086
BINDING SITE FOR RESIDUE CL H1174
12
BC3
SOFTWARE
HOH F:2055 , HOH F:2059 , ASP H:63 , HOH H:2028 , HOH H:2029
BINDING SITE FOR RESIDUE CA H2173
13
BC4
SOFTWARE
HOH A:2013 , ILE I:111
BINDING SITE FOR RESIDUE CL I1175
14
BC5
SOFTWARE
HOH A:2105 , HOH D:2164 , HOH I:2036 , HOH I:2105 , HOH I:2107 , HOH I:2108 , HOH I:2109
BINDING SITE FOR RESIDUE CA I1176
15
BC6
SOFTWARE
ASP I:63 , HOH I:2022 , HOH I:2049 , HOH I:2055 , HOH I:2056 , HOH K:2058 , HOH K:2059
BINDING SITE FOR RESIDUE CA I2173
16
BC7
SOFTWARE
ASP J:63 , HOH J:2015 , HOH J:2033 , HOH J:2035 , HOH L:2043 , HOH L:2044
BINDING SITE FOR RESIDUE CA J2173
17
BC8
SOFTWARE
GLU F:112 , LEU F:166 , HOH F:2097 , HOH F:2098 , HOH F:2127 , ASP K:24 , GLU K:139
BINDING SITE FOR RESIDUE CA K1175
18
BC9
SOFTWARE
HOH I:2064 , HOH I:2065 , ASP K:63 , HOH K:2043 , HOH K:2044
BINDING SITE FOR RESIDUE CA K2173
19
CC1
SOFTWARE
HOH J:2043 , HOH J:2044 , ASP L:63 , GLU L:67 , HOH L:2032 , HOH L:2038
BINDING SITE FOR RESIDUE CA L2173
20
CC2
SOFTWARE
GLY C:54 , HOH C:2125 , GLY E:54 , HOH E:2133 , HOH E:2140 , HOH E:2141 , HOH E:2142 , ARG L:53 , GLY L:54
BINDING SITE FOR RESIDUE EPE E1174
21
CC3
SOFTWARE
GLY D:54 , HOH D:2161 , GLY G:54 , HOH G:2125 , HOH H:2088 , GLY I:54 , HOH I:2142 , HOH I:2150
BINDING SITE FOR RESIDUE EPE I1174
22
CC4
SOFTWARE
ARG F:53 , GLY F:54 , HOH F:2126 , ARG J:53 , GLY J:54 , HOH J:2113 , HOH J:2114 , HOH J:2115 , HOH J:2116
BINDING SITE FOR RESIDUE EPE J1174
23
CC5
SOFTWARE
GLY A:54 , HOH A:2144 , GLU G:112 , ARG H:53 , GLY H:54 , HOH H:2119 , ARG K:53 , GLY K:54 , HOH K:2137 , HOH K:2147 , HOH K:2148
BINDING SITE FOR RESIDUE EPE K1174
[
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_d1umna_ (A:)
1b: SCOP_d1umnb_ (B:)
1c: SCOP_d1umnc_ (C:)
1d: SCOP_d1umnd_ (D:)
1e: SCOP_d1umne_ (E:)
1f: SCOP_d1umnf_ (F:)
1g: SCOP_d1umng_ (G:)
1h: SCOP_d1umnh_ (H:)
1i: SCOP_d1umni_ (I:)
1j: SCOP_d1umnj_ (J:)
1k: SCOP_d1umnk_ (K:)
1l: SCOP_d1umnl_ (L:)
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
:
Dodecameric ferritin homolog
(44)
Streptococcus suis [TaxId: 1307]
(8)
1a
d1umna_
A:
1b
d1umnb_
B:
1c
d1umnc_
C:
1d
d1umnd_
D:
1e
d1umne_
E:
1f
d1umnf_
F:
1g
d1umng_
G:
1h
d1umnh_
H:
1i
d1umni_
I:
1j
d1umnj_
J:
1k
d1umnk_
K:
1l
d1umnl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1umnG00 (G:8-172)
1b: CATH_1umnI00 (I:20-172)
1c: CATH_1umnD00 (D:21-172)
1d: CATH_1umnE00 (E:21-172)
1e: CATH_1umnJ00 (J:21-172)
1f: CATH_1umnK00 (K:21-172)
1g: CATH_1umnA00 (A:22-172)
1h: CATH_1umnB00 (B:22-172)
1i: CATH_1umnC00 (C:22-172)
1j: CATH_1umnF00 (F:22-172)
1k: CATH_1umnH00 (H:22-172)
1l: CATH_1umnL00 (L: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
1umnG00
G:8-172
1b
1umnI00
I:20-172
1c
1umnD00
D:21-172
1d
1umnE00
E:21-172
1e
1umnJ00
J:21-172
1f
1umnK00
K:21-172
1g
1umnA00
A:22-172
1h
1umnB00
B:22-172
1i
1umnC00
C:22-172
1j
1umnF00
F:22-172
1k
1umnH00
H:22-172
1l
1umnL00
L:22-172
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_1umnL01 (L:26-172)
1b: PFAM_Ferritin_1umnL02 (L:26-172)
1c: PFAM_Ferritin_1umnL03 (L:26-172)
1d: PFAM_Ferritin_1umnL04 (L:26-172)
1e: PFAM_Ferritin_1umnL05 (L:26-172)
1f: PFAM_Ferritin_1umnL06 (L:26-172)
1g: PFAM_Ferritin_1umnL07 (L:26-172)
1h: PFAM_Ferritin_1umnL08 (L:26-172)
1i: PFAM_Ferritin_1umnL09 (L:26-172)
1j: PFAM_Ferritin_1umnL10 (L:26-172)
1k: PFAM_Ferritin_1umnL11 (L:26-172)
1l: PFAM_Ferritin_1umnL12 (L:26-172)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Streptococcus suis
(7)
1a
Ferritin-1umnL01
L:26-172
1b
Ferritin-1umnL02
L:26-172
1c
Ferritin-1umnL03
L:26-172
1d
Ferritin-1umnL04
L:26-172
1e
Ferritin-1umnL05
L:26-172
1f
Ferritin-1umnL06
L:26-172
1g
Ferritin-1umnL07
L:26-172
1h
Ferritin-1umnL08
L:26-172
1i
Ferritin-1umnL09
L:26-172
1j
Ferritin-1umnL10
L:26-172
1k
Ferritin-1umnL11
L:26-172
1l
Ferritin-1umnL12
L:26-172
[
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 (336 KB)
Header - Asym.Unit
Biol.Unit 1 (328 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
1UMN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help