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2BW1
Asym. Unit
Info
Asym.Unit (339 KB)
Biol.Unit 1 (331 KB)
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(1)
Title
:
IRON-BOUND CRYSTAL STRUCTURE OF DPS-LIKE PEROXIDE RESISTANCE PROTEIN (DPR) FROM STREPTOCOCCUS SUIS.
Authors
:
A. Kauko, A. Pulliainen, S. Haataja, J. Finne, A. C. Papageorgiou
Date
:
07 Jul 05 (Deposition) - 27 Sep 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.81
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
:
Dpr, Peroxide Resistance, Iron-Binding, Ferroxidase, Dps- Family, Ferritin-Like
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kauko, A. 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
[
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]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEd)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
3e: FE (III) ION (FEe)
3f: FE (III) ION (FEf)
3g: FE (III) ION (FEg)
3h: FE (III) ION (FEh)
3i: FE (III) ION (FEi)
3j: FE (III) ION (FEj)
3k: FE (III) ION (FEk)
3l: FE (III) ION (FEl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3
FE
12
Ligand/Ion
FE (III) ION
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:47 , HOH A:2034 , ASP C:74 , GLU C:78 , HOH C:2053
BINDING SITE FOR RESIDUE FE A2000
02
AC2
SOFTWARE
HIS B:47 , HOH B:2036 , ASP D:74 , GLU D:78
BINDING SITE FOR RESIDUE FE B2000
03
AC3
SOFTWARE
ASP A:74 , GLU A:78 , HIS C:47 , HOH C:2028 , HOH C:2036
BINDING SITE FOR RESIDUE FE C2000
04
AC4
SOFTWARE
ASP B:74 , GLU B:78 , HIS D:47 , HOH D:2034 , HOH D:2042
BINDING SITE FOR RESIDUE FE D2000
05
AC5
SOFTWARE
HIS E:47 , HOH E:2042 , ASP G:74 , GLU G:78 , HOH G:2071
BINDING SITE FOR RESIDUE FE E2000
06
AC6
SOFTWARE
HIS F:47 , HOH F:2026 , HOH F:2031 , ASP H:74 , GLU H:78
BINDING SITE FOR RESIDUE FE F2000
07
AC7
SOFTWARE
ASP E:74 , GLU E:78 , HOH E:2059 , HIS G:47 , HOH G:2036
BINDING SITE FOR RESIDUE FE G2000
08
AC8
SOFTWARE
ASP F:74 , GLU F:78 , HIS H:47 , HOH H:2018 , HOH H:2023
BINDING SITE FOR RESIDUE FE H2000
09
AC9
SOFTWARE
HIS I:47 , HOH I:2034 , ASP K:74 , GLU K:78
BINDING SITE FOR RESIDUE FE I2000
10
BC1
SOFTWARE
HIS J:47 , HOH J:2030 , ASP L:74 , GLU L:78
BINDING SITE FOR RESIDUE FE J2000
11
BC2
SOFTWARE
ASP I:74 , GLU I:78 , HOH I:2052 , HOH I:2059 , HIS K:47
BINDING SITE FOR RESIDUE FE K2000
12
BC3
SOFTWARE
ASP J:74 , GLU J:78 , HOH J:2042 , HIS L:47
BINDING SITE FOR RESIDUE FE L2000
13
BC4
SOFTWARE
LEU F:166 , HOH F:2067 , HOH F:2091 , ASP K:24 , GLU K:139 , HOH K:2002
BINDING SITE FOR RESIDUE CA K1501
14
BC5
SOFTWARE
HOH A:2144 , HOH A:2145 , GLY C:54 , HOH C:2117 , GLY E:54 , ILE E:57 , ASP E:137 , GLU E:138 , HOH E:2120 , GLY L:54 , ILE L:57 , HOH L:2114
BINDING SITE FOR RESIDUE EPE A 200
15
BC6
SOFTWARE
HOH B:2126 , HOH B:2127 , GLY D:54 , GLY G:54 , HOH G:2138 , GLY I:54 , ILE I:57 , HOH I:2119
BINDING SITE FOR RESIDUE EPE B 200
16
BC7
SOFTWARE
GLY B:54 , ILE B:57 , HOH B:2025 , HOH B:2121 , HOH C:2124 , ARG F:53 , GLY F:54 , ILE F:57 , HOH F:2089 , ARG J:53 , GLY J:54 , HOH J:2089 , ASP K:137 , GLU K:138
BINDING SITE FOR RESIDUE EPE C 200
17
BC8
SOFTWARE
GLY A:54 , ILE A:57 , HOH A:2028 , HOH A:2131 , HOH D:2149 , HOH D:2150 , HOH D:2151 , GLU G:112 , HOH G:2098 , ARG H:53 , GLY H:54 , ILE H:57 , ARG K:53 , GLY K:54 , HOH K:2103 , HOH K:2140
BINDING SITE FOR RESIDUE EPE D 200
[
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)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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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_d2bw1a_ (A:)
1b: SCOP_d2bw1b_ (B:)
1c: SCOP_d2bw1c_ (C:)
1d: SCOP_d2bw1d_ (D:)
1e: SCOP_d2bw1e_ (E:)
1f: SCOP_d2bw1f_ (F:)
1g: SCOP_d2bw1g_ (G:)
1h: SCOP_d2bw1h_ (H:)
1i: SCOP_d2bw1i_ (I:)
1j: SCOP_d2bw1j_ (J:)
1k: SCOP_d2bw1k_ (K:)
1l: SCOP_d2bw1l_ (L:)
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)
(
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)
(
)
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(
)
(
)
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
d2bw1a_
A:
1b
d2bw1b_
B:
1c
d2bw1c_
C:
1d
d2bw1d_
D:
1e
d2bw1e_
E:
1f
d2bw1f_
F:
1g
d2bw1g_
G:
1h
d2bw1h_
H:
1i
d2bw1i_
I:
1j
d2bw1j_
J:
1k
d2bw1k_
K:
1l
d2bw1l_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2bw1G00 (G:8-172)
1b: CATH_2bw1K00 (K:20-172)
1c: CATH_2bw1D00 (D:21-172)
1d: CATH_2bw1A00 (A:22-172)
1e: CATH_2bw1B00 (B:22-172)
1f: CATH_2bw1C00 (C:22-172)
1g: CATH_2bw1E00 (E:22-172)
1h: CATH_2bw1F00 (F:22-172)
1i: CATH_2bw1H00 (H:22-172)
1j: CATH_2bw1I00 (I:22-172)
1k: CATH_2bw1J00 (J:22-172)
1l: CATH_2bw1L00 (L:22-172)
View:
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(
)
(
)
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
2bw1G00
G:8-172
1b
2bw1K00
K:20-172
1c
2bw1D00
D:21-172
1d
2bw1A00
A:22-172
1e
2bw1B00
B:22-172
1f
2bw1C00
C:22-172
1g
2bw1E00
E:22-172
1h
2bw1F00
F:22-172
1i
2bw1H00
H:22-172
1j
2bw1I00
I:22-172
1k
2bw1J00
J:22-172
1l
2bw1L00
L:22-172
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (339 KB)
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