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2IY4
Biol. Unit 2
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
(0, 0)
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:
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Sites
(13, 13)
Info
All Sites
01: BC3 (SOFTWARE)
02: BC4 (SOFTWARE)
03: BC5 (SOFTWARE)
04: BC6 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC3
SOFTWARE
HIS M:31 , ASP M:47 , HOH M:2021 , ASP O:58 , GLU O:62
BINDING SITE FOR RESIDUE FE M1157
02
BC4
SOFTWARE
ASP M:58 , GLU M:62 , HIS O:31
BINDING SITE FOR RESIDUE FE M1158
03
BC5
SOFTWARE
ASP N:58 , GLU N:62 , HIS P:31
BINDING SITE FOR RESIDUE FE N1157
04
BC6
SOFTWARE
GLU N:59 , ARG N:63
BINDING SITE FOR RESIDUE FE N1158
05
BC7
SOFTWARE
HIS N:31 , ASP P:58 , GLU P:62 , HOH P:2029
BINDING SITE FOR RESIDUE FE P1157
06
BC8
SOFTWARE
HIS Q:31 , ASP S:58 , GLU S:62
BINDING SITE FOR RESIDUE FE Q1157
07
BC9
SOFTWARE
ASP R:58 , GLU R:62 , HIS T:31 , ASP T:47
BINDING SITE FOR RESIDUE FE R1157
08
CC1
SOFTWARE
HIS R:31 , ASP T:58 , GLU T:62
BINDING SITE FOR RESIDUE FE R1158
09
CC2
SOFTWARE
ARG N:63 , HOH N:2028 , ALA S:137 , ASP S:140
BINDING SITE FOR RESIDUE FE S1157
10
CC3
SOFTWARE
ASP U:58 , GLU U:62 , HIS X:31
BINDING SITE FOR RESIDUE FE U1157
11
CC4
SOFTWARE
ASP V:58 , GLU V:62 , HIS Y:31 , ASP Y:47
BINDING SITE FOR RESIDUE FE V1157
12
CC5
SOFTWARE
HIS U:31 , ASP X:58 , GLU X:62 , HOH X:2034
BINDING SITE FOR RESIDUE FE X1157
13
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 only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: DPS_1 (M:31-47,N:31-47,O:31-47,P:31-47,Q:...)
2: DPS_2 (M:57-71,N:57-71,O:57-71,P:57-71,Q:...)
;
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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
12
-
-
-
-
-
-
-
-
-
-
-
-
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
12
-
-
-
-
-
-
-
-
-
-
-
-
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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All Exon Boundaries
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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.
(no "Exon" information available for biological units yet)
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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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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)
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)
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)
Info
all PFAM domains
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