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Asym. Unit
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Asym.Unit (631 KB)
Biol.Unit 1 (613 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF STREPTOCOCCUS SUIS DPR WITH COBALT
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
:
2.30
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, 27)
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)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: COBALT (II) ION (COa)
3b: COBALT (II) ION (COb)
3c: COBALT (II) ION (COc)
3d: COBALT (II) ION (COd)
3e: COBALT (II) ION (COe)
3f: COBALT (II) ION (COf)
3g: COBALT (II) ION (COg)
3h: COBALT (II) ION (COh)
3i: COBALT (II) ION (COi)
3j: COBALT (II) ION (COj)
3k: COBALT (II) ION (COk)
3l: COBALT (II) ION (COl)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
4c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
4d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
CO
12
Ligand/Ion
COBALT (II) ION
4
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:74 , GLU A:78 , HOH A:2063 , HIS C:47
BINDING SITE FOR RESIDUE CO A1173
02
AC2
SOFTWARE
ALA A:169 , PRO A:170 , LYS A:171 , GLY I:84 , HOH K:2008
BINDING SITE FOR RESIDUE CL A1174
03
AC3
SOFTWARE
ASP B:74 , GLU B:78 , HOH B:2093 , HIS D:47 , HOH D:2022
BINDING SITE FOR RESIDUE CO B1173
04
AC4
SOFTWARE
GLU B:113 , HOH B:2058 , HOH K:2054
BINDING SITE FOR RESIDUE CA B1174
05
AC5
SOFTWARE
HIS A:47 , HOH A:2014 , ASP C:74 , GLU C:78
BINDING SITE FOR RESIDUE CO C1173
06
AC6
SOFTWARE
HOH L:2049 , HOH L:2050 , HOH L:2051
BINDING SITE FOR RESIDUE CA C1174
07
AC7
SOFTWARE
HIS B:47 , ASP D:74 , GLU D:78 , HOH D:2088 , HOH D:2089
BINDING SITE FOR RESIDUE CO D1173
08
AC8
SOFTWARE
ARG C:53 , GLY C:54 , ILE C:57 , GLY E:54 , ASP E:137 , HOH E:2038 , HOH E:2043 , GLY L:54
BINDING SITE FOR RESIDUE EPE E1173
09
AC9
SOFTWARE
ASP E:74 , GLU E:78 , HOH E:2022 , HIS G:47
BINDING SITE FOR RESIDUE CO E1174
10
BC1
SOFTWARE
LEU C:166 , ALA E:23 , GLU E:139
BINDING SITE FOR RESIDUE CA E1175
11
BC2
SOFTWARE
ASP F:74 , GLU F:78 , HIS H:47
BINDING SITE FOR RESIDUE CO F1173
12
BC3
SOFTWARE
LEU F:166 , HOH F:2064 , HOH F:2065 , ASP K:24 , GLU K:139 , HOH K:2058
BINDING SITE FOR RESIDUE CA F1174
13
BC4
SOFTWARE
HOH F:2037
BINDING SITE FOR RESIDUE CA F1175
14
BC5
SOFTWARE
HIS E:47 , ASP G:74 , GLU G:78 , HOH G:2022 , HOH G:2052
BINDING SITE FOR RESIDUE CO G1173
15
BC6
SOFTWARE
HIS F:47 , HOH F:2017 , ASP H:74 , GLU H:78
BINDING SITE FOR RESIDUE CO H1173
16
BC7
SOFTWARE
ASN G:108 , HOH K:2070
BINDING SITE FOR RESIDUE CA H1176
17
BC8
SOFTWARE
HOH D:2082 , ARG G:53 , GLY G:54 , HOH G:2045 , GLY I:54 , HOH I:2064
BINDING SITE FOR RESIDUE EPE I1173
18
BC9
SOFTWARE
ASP I:74 , GLU I:78 , HOH I:2027 , HIS K:47
BINDING SITE FOR RESIDUE CO I1174
19
CC1
SOFTWARE
ALA I:169
BINDING SITE FOR RESIDUE CL I1175
20
CC2
SOFTWARE
ASN A:108 , HOH I:2042 , HOH I:2043
BINDING SITE FOR RESIDUE CA I1176
21
CC3
SOFTWARE
GLY B:54 , HOH B:2085 , GLY F:54 , HOH F:2063 , GLY J:54 , HOH J:2067 , HOH J:2072 , HOH J:2073 , ASP K:137
BINDING SITE FOR RESIDUE EPE J1173
22
CC4
SOFTWARE
ASP J:74 , GLU J:78 , HOH J:2035 , HIS L:47
BINDING SITE FOR RESIDUE CO J1174
23
CC5
SOFTWARE
HOH J:2021
BINDING SITE FOR RESIDUE CL J1175
24
CC6
SOFTWARE
HOH B:2087 , HOH J:2019 , HOH J:2047 , HOH J:2048
BINDING SITE FOR RESIDUE CA J1176
25
CC7
SOFTWARE
GLY A:54 , GLU G:112 , ARG H:53 , GLY H:54 , HOH H:2050 , ARG K:53 , GLY K:54
BINDING SITE FOR RESIDUE EPE K1173
26
CC8
SOFTWARE
HIS I:47 , ASP K:74 , GLU K:78
BINDING SITE FOR RESIDUE CO K1174
27
CC9
SOFTWARE
HIS J:47 , ASP L:74 , GLU L:78 , HOH L:2030 , HOH L:2070
BINDING SITE FOR RESIDUE CO L1173
[
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
;
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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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_d2xjma_ (A:)
1b: SCOP_d2xjmb_ (B:)
1c: SCOP_d2xjmc_ (C:)
1d: SCOP_d2xjmd_ (D:)
1e: SCOP_d2xjme_ (E:)
1f: SCOP_d2xjmf_ (F:)
1g: SCOP_d2xjmg_ (G:)
1h: SCOP_d2xjmh_ (H:)
1i: SCOP_d2xjmi_ (I:)
1j: SCOP_d2xjmj_ (J:)
1k: SCOP_d2xjmk_ (K:)
1l: SCOP_d2xjml_ (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
d2xjma_
A:
1b
d2xjmb_
B:
1c
d2xjmc_
C:
1d
d2xjmd_
D:
1e
d2xjme_
E:
1f
d2xjmf_
F:
1g
d2xjmg_
G:
1h
d2xjmh_
H:
1i
d2xjmi_
I:
1j
d2xjmj_
J:
1k
d2xjmk_
K:
1l
d2xjml_
L:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_2xjmL01 (L:26-172)
1b: PFAM_Ferritin_2xjmL02 (L:26-172)
1c: PFAM_Ferritin_2xjmL03 (L:26-172)
1d: PFAM_Ferritin_2xjmL04 (L:26-172)
1e: PFAM_Ferritin_2xjmL05 (L:26-172)
1f: PFAM_Ferritin_2xjmL06 (L:26-172)
1g: PFAM_Ferritin_2xjmL07 (L:26-172)
1h: PFAM_Ferritin_2xjmL08 (L:26-172)
1i: PFAM_Ferritin_2xjmL09 (L:26-172)
1j: PFAM_Ferritin_2xjmL10 (L:26-172)
1k: PFAM_Ferritin_2xjmL11 (L:26-172)
1l: PFAM_Ferritin_2xjmL12 (L:26-172)
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Clans
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Families
(
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)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Streptococcus suis
(7)
1a
Ferritin-2xjmL01
L:26-172
1b
Ferritin-2xjmL02
L:26-172
1c
Ferritin-2xjmL03
L:26-172
1d
Ferritin-2xjmL04
L:26-172
1e
Ferritin-2xjmL05
L:26-172
1f
Ferritin-2xjmL06
L:26-172
1g
Ferritin-2xjmL07
L:26-172
1h
Ferritin-2xjmL08
L:26-172
1i
Ferritin-2xjmL09
L:26-172
1j
Ferritin-2xjmL10
L:26-172
1k
Ferritin-2xjmL11
L:26-172
1l
Ferritin-2xjmL12
L:26-172
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