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2IY4
Asym. Unit
Info
Asym.Unit (627 KB)
Biol.Unit 1 (311 KB)
Biol.Unit 2 (315 KB)
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(1)
Title
:
X-RAY STRUCTURE OF DPS FROM LISTERIA MONOCYTOGENES
Authors
:
A. Ilari, G. Bellapadrona, S. Stefanini, E. Chiancone
Date
:
12 Jul 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Biol. Unit 2: M,N,O,P,Q,R,S,T,U,V,X,Y (1x)
Keywords
:
Iron, Iron Storage, Metal-Binding, Oxidative Damage, Dpslm (Dna-Binding Protein From Starved Cells) From Lister Iron- Incorporation, Metal-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Bellapadrona, R. Chiaraluce, V. Consalvi, A. Ilari, S. Stefanini, E. Chiancone
The Mutations Lys 114 --> Gln And Asp 126 --> Asn Disrupt An Intersubunit Salt Bridge And Convert Listeria Innocua Dps Into Its Natural Mutant Listeria Monocytogenes Dps. Effects On Protein Stability At Low Ph.
Proteins V. 66 975 2007
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Hetero Components
(1, 24)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
1i: FE (III) ION (FEi)
1j: FE (III) ION (FEj)
1k: FE (III) ION (FEk)
1l: FE (III) ION (FEl)
1m: FE (III) ION (FEm)
1n: FE (III) ION (FEn)
1o: FE (III) ION (FEo)
1p: FE (III) ION (FEp)
1q: FE (III) ION (FEq)
1r: FE (III) ION (FEr)
1s: FE (III) ION (FEs)
1t: FE (III) ION (FEt)
1u: FE (III) ION (FEu)
1v: FE (III) ION (FEv)
1w: FE (III) ION (FEw)
1x: FE (III) ION (FEx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
24
Ligand/Ion
FE (III) ION
[
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:58 , GLU B:62 , HIS D:31
BINDING SITE FOR RESIDUE FE B1157
02
AC2
SOFTWARE
HIS A:31 , ASP C:58 , GLU C:62
BINDING SITE FOR RESIDUE FE C1157
03
AC3
SOFTWARE
HIS B:31 , ASP D:58 , GLU D:62
BINDING SITE FOR RESIDUE FE D1157
04
AC4
SOFTWARE
ASP E:58 , GLU E:62 , HIS G:31 , ASP G:47
BINDING SITE FOR RESIDUE FE E1157
05
AC5
SOFTWARE
HIS E:31 , ASP E:47 , ASP G:58 , GLU G:62
BINDING SITE FOR RESIDUE FE E1158
06
AC6
SOFTWARE
ASP F:58 , GLU F:62 , HOH F:2036 , HIS H:31
BINDING SITE FOR RESIDUE FE F1157
07
AC7
SOFTWARE
HIS F:31 , ASP H:58 , GLU H:62
BINDING SITE FOR RESIDUE FE H1157
08
AC8
SOFTWARE
ASP I:58 , GLU I:62 , HIS K:31
BINDING SITE FOR RESIDUE FE I1157
09
AC9
SOFTWARE
ASP J:58 , GLU J:62 , HIS L:31
BINDING SITE FOR RESIDUE FE J1157
10
BC1
SOFTWARE
HIS I:31 , ASP K:58 , GLU K:62
BINDING SITE FOR RESIDUE FE K1157
11
BC2
SOFTWARE
HIS J:31 , ASP L:58 , GLU L:62
BINDING SITE FOR RESIDUE FE L1157
12
BC3
SOFTWARE
HIS M:31 , ASP M:47 , HOH M:2021 , ASP O:58 , GLU O:62
BINDING SITE FOR RESIDUE FE M1157
13
BC4
SOFTWARE
ASP M:58 , GLU M:62 , HIS O:31
BINDING SITE FOR RESIDUE FE M1158
14
BC5
SOFTWARE
ASP N:58 , GLU N:62 , HIS P:31
BINDING SITE FOR RESIDUE FE N1157
15
BC6
SOFTWARE
GLU N:59 , ARG N:63
BINDING SITE FOR RESIDUE FE N1158
16
BC7
SOFTWARE
HIS N:31 , ASP P:58 , GLU P:62 , HOH P:2029
BINDING SITE FOR RESIDUE FE P1157
17
BC8
SOFTWARE
HIS Q:31 , ASP S:58 , GLU S:62
BINDING SITE FOR RESIDUE FE Q1157
18
BC9
SOFTWARE
ASP R:58 , GLU R:62 , HIS T:31 , ASP T:47
BINDING SITE FOR RESIDUE FE R1157
19
CC1
SOFTWARE
HIS R:31 , ASP T:58 , GLU T:62
BINDING SITE FOR RESIDUE FE R1158
20
CC2
SOFTWARE
ARG N:63 , HOH N:2028 , ALA S:137 , ASP S:140
BINDING SITE FOR RESIDUE FE S1157
21
CC3
SOFTWARE
ASP U:58 , GLU U:62 , HIS X:31
BINDING SITE FOR RESIDUE FE U1157
22
CC4
SOFTWARE
ASP V:58 , GLU V:62 , HIS Y:31 , ASP Y:47
BINDING SITE FOR RESIDUE FE V1157
23
CC5
SOFTWARE
HIS U:31 , ASP X:58 , GLU X:62 , HOH X:2034
BINDING SITE FOR RESIDUE FE X1157
24
CC6
SOFTWARE
HIS V:31 , ASP V:47 , HOH V:2023 , ASP Y:58 , GLU Y:62
BINDING SITE FOR RESIDUE FE Y1157
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 48)
Info
All PROSITE Patterns/Profiles
1: DPS_1 (A:31-47,B:31-47,C:31-47,D:31-47,E:...)
2: DPS_2 (A:57-71,B:57-71,C:57-71,D:57-71,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DPS_1
PS00818
Dps protein family signature 1.
DPS_LISMO
31-47
24
A:31-47
B:31-47
C:31-47
D:31-47
E:31-47
F:31-47
G:31-47
H:31-47
I:31-47
J:31-47
K:31-47
L:31-47
M:31-47
N:31-47
O:31-47
P:31-47
Q:31-47
R:31-47
S:31-47
T:31-47
U:31-47
V:31-47
X:31-47
Y:31-47
2
DPS_2
PS00819
Dps protein family signature 2.
DPS_LISMO
57-71
24
A:57-71
B:57-71
C:57-71
D:57-71
E:57-71
F:57-71
G:57-71
H:57-71
I:57-71
J:57-71
K:57-71
L:57-71
M:57-71
N:57-71
O:57-71
P:57-71
Q:57-71
R:57-71
S:57-71
T:57-71
U:57-71
V:57-71
X:57-71
Y:57-71
[
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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, 24)
Info
All SCOP Domains
1a: SCOP_d2iy4a_ (A:)
1b: SCOP_d2iy4b_ (B:)
1c: SCOP_d2iy4k_ (K:)
1d: SCOP_d2iy4l_ (L:)
1e: SCOP_d2iy4m_ (M:)
1f: SCOP_d2iy4n_ (N:)
1g: SCOP_d2iy4o_ (O:)
1h: SCOP_d2iy4p_ (P:)
1i: SCOP_d2iy4q_ (Q:)
1j: SCOP_d2iy4r_ (R:)
1k: SCOP_d2iy4s_ (S:)
1l: SCOP_d2iy4t_ (T:)
1m: SCOP_d2iy4c_ (C:)
1n: SCOP_d2iy4u_ (U:)
1o: SCOP_d2iy4v_ (V:)
1p: SCOP_d2iy4x_ (X:)
1q: SCOP_d2iy4y_ (Y:)
1r: SCOP_d2iy4d_ (D:)
1s: SCOP_d2iy4e_ (E:)
1t: SCOP_d2iy4f_ (F:)
1u: SCOP_d2iy4g_ (G:)
1v: SCOP_d2iy4h_ (H:)
1w: SCOP_d2iy4i_ (I:)
1x: SCOP_d2iy4j_ (J:)
View:
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Classes
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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
:
automated matches
(70)
Listeria monocytogenes [TaxId: 1639]
(1)
1a
d2iy4a_
A:
1b
d2iy4b_
B:
1c
d2iy4k_
K:
1d
d2iy4l_
L:
1e
d2iy4m_
M:
1f
d2iy4n_
N:
1g
d2iy4o_
O:
1h
d2iy4p_
P:
1i
d2iy4q_
Q:
1j
d2iy4r_
R:
1k
d2iy4s_
S:
1l
d2iy4t_
T:
1m
d2iy4c_
C:
1n
d2iy4u_
U:
1o
d2iy4v_
V:
1p
d2iy4x_
X:
1q
d2iy4y_
Y:
1r
d2iy4d_
D:
1s
d2iy4e_
E:
1t
d2iy4f_
F:
1u
d2iy4g_
G:
1v
d2iy4h_
H:
1w
d2iy4i_
I:
1x
d2iy4j_
J:
[
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]
CATH Domains
(1, 24)
Info
all CATH domains
1a: CATH_2iy4U00 (U:3-156)
1b: CATH_2iy4A00 (A:6-156)
1c: CATH_2iy4D00 (D:7-156)
1d: CATH_2iy4E00 (E:7-156)
1e: CATH_2iy4H00 (H:7-156)
1f: CATH_2iy4I00 (I:7-156)
1g: CATH_2iy4J00 (J:7-156)
1h: CATH_2iy4K00 (K:7-156)
1i: CATH_2iy4L00 (L:7-156)
1j: CATH_2iy4N00 (N:7-156)
1k: CATH_2iy4P00 (P:7-156)
1l: CATH_2iy4T00 (T:7-156)
1m: CATH_2iy4C00 (C:6-156)
1n: CATH_2iy4V00 (V:7-156)
1o: CATH_2iy4X00 (X:7-156)
1p: CATH_2iy4Y00 (Y:7-156)
1q: CATH_2iy4M00 (M:8-156)
1r: CATH_2iy4F00 (F:6-156)
1s: CATH_2iy4G00 (G:6-156)
1t: CATH_2iy4O00 (O:6-156)
1u: CATH_2iy4Q00 (Q:6-156)
1v: CATH_2iy4R00 (R:6-156)
1w: CATH_2iy4S00 (S:6-156)
1x: CATH_2iy4B00 (B:7-156)
View:
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Classes
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Listeria monocytogenes. Organism_taxid: 1639.
(1)
1a
2iy4U00
U:3-156
1b
2iy4A00
A:6-156
1c
2iy4D00
D:7-156
1d
2iy4E00
E:7-156
1e
2iy4H00
H:7-156
1f
2iy4I00
I:7-156
1g
2iy4J00
J:7-156
1h
2iy4K00
K:7-156
1i
2iy4L00
L:7-156
1j
2iy4N00
N:7-156
1k
2iy4P00
P:7-156
1l
2iy4T00
T:7-156
1m
2iy4C00
C:6-156
1n
2iy4V00
V:7-156
1o
2iy4X00
X:7-156
1p
2iy4Y00
Y:7-156
1q
2iy4M00
M:8-156
1r
2iy4F00
F:6-156
1s
2iy4G00
G:6-156
1t
2iy4O00
O:6-156
1u
2iy4Q00
Q:6-156
1v
2iy4R00
R:6-156
1w
2iy4S00
S:6-156
1x
2iy4B00
B:7-156
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Pfam Domains
(0, 0)
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all PFAM domains
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