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2XJO
Asym. Unit
Info
Asym.Unit (644 KB)
Biol.Unit 1 (625 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF STREPTOCOCCUS SUIS DPR WITH NICKEL
Authors
:
T. Haikarainen, A. Thanassoulas, P. Stavros, G. Nounesis, S. Haataja, A. C. Papageorgiou
Date
:
06 Jul 10 (Deposition) - 24 Nov 10 (Release) - 12 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
:
Oxidoreductase, Iron Storage, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Haikarainen, A. Thanassoulas, P. Stavros, G. Nounesis, S. Haataja A. C. Papageorgiou
Structural And Thermodynamic Characterization Of Metal Ion Binding In Streptococcus Suis Dpr.
J. Mol. Biol. V. 405 448 2011
[
close entry info
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Hetero Components
(4, 29)
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)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
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)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
4c: NICKEL (II) ION (NIc)
4d: NICKEL (II) ION (NId)
4e: NICKEL (II) ION (NIe)
4f: NICKEL (II) ION (NIf)
4g: NICKEL (II) ION (NIg)
4h: NICKEL (II) ION (NIh)
4i: NICKEL (II) ION (NIi)
4j: NICKEL (II) ION (NIj)
4k: NICKEL (II) ION (NIk)
4l: NICKEL (II) ION (NIl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
7
Ligand/Ion
CALCIUM ION
2
CL
6
Ligand/Ion
CHLORIDE ION
3
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
4
NI
12
Ligand/Ion
NICKEL (II) ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:74 , GLU A:78 , HOH A:2025 , HIS C:47 , HOH C:2011
BINDING SITE FOR RESIDUE NI A1173
02
AC2
SOFTWARE
GLY B:54 , ILE B:57 , HOH B:2084 , HOH B:2092 , ARG F:53 , GLY F:54 , HOH F:2071 , GLY J:54 , HOH J:2056 , ASP K:137
BINDING SITE FOR RESIDUE EPE B1173
03
AC3
SOFTWARE
ASP B:74 , GLU B:78 , HOH B:2033 , HIS D:47 , HOH D:2024
BINDING SITE FOR RESIDUE NI B1174
04
AC4
SOFTWARE
GLU B:113 , HOH B:2057 , HOH B:2062 , HOH K:2051
BINDING SITE FOR RESIDUE CA B1175
05
AC5
SOFTWARE
ALA B:169 , LYS B:171 , GLY L:84
BINDING SITE FOR RESIDUE CL B1176
06
AC6
SOFTWARE
HIS A:47 , HOH A:2014 , HOH A:2017 , ASP C:74 , GLU C:78
BINDING SITE FOR RESIDUE NI C1173
07
AC7
SOFTWARE
HIS B:47 , ASP D:74 , GLU D:78 , HOH D:2037 , HOH D:2042
BINDING SITE FOR RESIDUE NI D1173
08
AC8
SOFTWARE
ILE D:111 , HOH D:2017
BINDING SITE FOR RESIDUE CL D1174
09
AC9
SOFTWARE
HOH D:2062 , HOH D:2065 , HOH G:2043
BINDING SITE FOR RESIDUE CA D1175
10
BC1
SOFTWARE
ASP E:74 , GLU E:78 , HIS G:47 , HOH G:2008 , HOH G:2011
BINDING SITE FOR RESIDUE NI E1173
11
BC2
SOFTWARE
GLY A:84 , ALA E:169 , LYS E:171
BINDING SITE FOR RESIDUE CL E1174
12
BC3
SOFTWARE
ASP F:74 , GLU F:78 , HOH F:2031 , HIS H:47 , HOH H:2014
BINDING SITE FOR RESIDUE NI F1173
13
BC4
SOFTWARE
LEU F:166 , HOH F:2044 , HOH F:2072 , HOH F:2073 , ASP K:24 , GLU K:139
BINDING SITE FOR RESIDUE CA F1174
14
BC5
SOFTWARE
HOH F:2042
BINDING SITE FOR RESIDUE CA F1175
15
BC6
SOFTWARE
GLY D:54 , ARG G:53 , GLY G:54 , ILE G:57 , HOH G:2046 , GLY I:54
BINDING SITE FOR RESIDUE EPE G1173
16
BC7
SOFTWARE
HIS E:47 , ASP G:74 , GLU G:78 , HOH G:2016 , HOH G:2018
BINDING SITE FOR RESIDUE NI G1174
17
BC8
SOFTWARE
GLY B:84 , HOH B:2037 , LYS G:171
BINDING SITE FOR RESIDUE CL G1175
18
BC9
SOFTWARE
HIS F:47 , HOH F:2020 , ASP H:74 , GLU H:78 , HOH H:2022
BINDING SITE FOR RESIDUE NI H1173
19
CC1
SOFTWARE
ASP I:74 , GLU I:78 , HOH I:2023 , HIS K:47 , HOH K:2014
BINDING SITE FOR RESIDUE NI I1173
20
CC2
SOFTWARE
ILE I:111 , HOH I:2007 , HOH I:2012
BINDING SITE FOR RESIDUE CL I1174
21
CC3
SOFTWARE
ASN A:108 , HOH I:2007 , HOH I:2039
BINDING SITE FOR RESIDUE CA I1175
22
CC4
SOFTWARE
ASP J:74 , GLU J:78 , HIS L:47 , HOH L:2012 , HOH L:2014
BINDING SITE FOR RESIDUE NI J1173
23
CC5
SOFTWARE
ILE J:111 , GLU J:112 , HOH J:2011
BINDING SITE FOR RESIDUE CL J1174
24
CC6
SOFTWARE
HOH B:2086 , HOH J:2039 , HOH J:2041
BINDING SITE FOR RESIDUE CA J1175
25
CC7
SOFTWARE
GLY A:54 , GLU G:112 , GLY H:54 , GLY K:54 , HOH K:2075
BINDING SITE FOR RESIDUE EPE K1173
26
CC8
SOFTWARE
HIS I:47 , HOH I:2015 , HOH I:2017 , ASP K:74 , GLU K:78
BINDING SITE FOR RESIDUE NI K1174
27
CC9
SOFTWARE
ASN G:108 , HOH G:2026 , HOH K:2068
BINDING SITE FOR RESIDUE CA K1175
28
DC1
SOFTWARE
ARG C:53 , GLY C:54 , ARG E:53 , GLY E:54 , ILE E:57 , GLU E:138 , HOH E:2005 , HOH E:2036 , ARG L:53 , GLY L:54 , HOH L:2055
BINDING SITE FOR RESIDUE EPE L1173
29
DC2
SOFTWARE
HIS J:47 , HOH J:2015 , ASP L:74 , GLU L:78 , HOH L:2024
BINDING SITE FOR RESIDUE NI L1174
[
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:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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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_d2xjoa_ (A:)
1b: SCOP_d2xjob_ (B:)
1c: SCOP_d2xjoc_ (C:)
1d: SCOP_d2xjod_ (D:)
1e: SCOP_d2xjoe_ (E:)
1f: SCOP_d2xjof_ (F:)
1g: SCOP_d2xjog_ (G:)
1h: SCOP_d2xjoh_ (H:)
1i: SCOP_d2xjoi_ (I:)
1j: SCOP_d2xjoj_ (J:)
1k: SCOP_d2xjok_ (K:)
1l: SCOP_d2xjol_ (L:)
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Classes
(
)
(
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(
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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
d2xjoa_
A:
1b
d2xjob_
B:
1c
d2xjoc_
C:
1d
d2xjod_
D:
1e
d2xjoe_
E:
1f
d2xjof_
F:
1g
d2xjog_
G:
1h
d2xjoh_
H:
1i
d2xjoi_
I:
1j
d2xjoj_
J:
1k
d2xjok_
K:
1l
d2xjol_
L:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_2xjoL01 (L:26-172)
1b: PFAM_Ferritin_2xjoL02 (L:26-172)
1c: PFAM_Ferritin_2xjoL03 (L:26-172)
1d: PFAM_Ferritin_2xjoL04 (L:26-172)
1e: PFAM_Ferritin_2xjoL05 (L:26-172)
1f: PFAM_Ferritin_2xjoL06 (L:26-172)
1g: PFAM_Ferritin_2xjoL07 (L:26-172)
1h: PFAM_Ferritin_2xjoL08 (L:26-172)
1i: PFAM_Ferritin_2xjoL09 (L:26-172)
1j: PFAM_Ferritin_2xjoL10 (L:26-172)
1k: PFAM_Ferritin_2xjoL11 (L:26-172)
1l: PFAM_Ferritin_2xjoL12 (L:26-172)
View:
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Streptococcus suis
(7)
1a
Ferritin-2xjoL01
L:26-172
1b
Ferritin-2xjoL02
L:26-172
1c
Ferritin-2xjoL03
L:26-172
1d
Ferritin-2xjoL04
L:26-172
1e
Ferritin-2xjoL05
L:26-172
1f
Ferritin-2xjoL06
L:26-172
1g
Ferritin-2xjoL07
L:26-172
1h
Ferritin-2xjoL08
L:26-172
1i
Ferritin-2xjoL09
L:26-172
1j
Ferritin-2xjoL10
L:26-172
1k
Ferritin-2xjoL11
L:26-172
1l
Ferritin-2xjoL12
L:26-172
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