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1JRE
Asym. Unit
Info
Asym.Unit (310 KB)
Biol.Unit 1 (302 KB)
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(1)
Title
:
DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN
Authors
:
J. Luo, D. Liu, M. A. White, R. O. Fox
Date
:
13 Aug 01 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
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
:
Dodecamer, Metal Bound Complex, Dna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Luo, D. Liu, M. A. White, R. O. Fox
Dna Protection And Binding By E. Coli Dps Protein
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 25)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
1i: CADMIUM ION (CDi)
1j: CADMIUM ION (CDj)
1k: CADMIUM ION (CDk)
1l: CADMIUM ION (CDl)
1m: CADMIUM ION (CDm)
2a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
2b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
2c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
2d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
2e: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSe)
2f: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSf)
2g: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSg)
2h: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSh)
2i: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSi)
2j: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSj)
2k: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSk)
2l: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
13
Ligand/Ion
CADMIUM ION
2
TRS
12
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:51 , ASP A:67 , HOH A:557 , HOH A:568 , HOH A:570 , GLU B:82
BINDING SITE FOR RESIDUE CD B 201
02
AC2
SOFTWARE
GLU A:82 , HOH A:590 , HOH A:603 , HIS B:51 , ASP B:67 , HOH B:575
BINDING SITE FOR RESIDUE CD A 201
03
AC3
SOFTWARE
HIS C:51 , ASP C:67 , HOH C:662 , GLU D:82 , HOH D:651
BINDING SITE FOR RESIDUE CD D 201
04
AC4
SOFTWARE
GLU C:82 , HOH C:681 , HOH C:693 , HIS D:51 , ASP D:67
BINDING SITE FOR RESIDUE CD C 201
05
AC5
SOFTWARE
HIS E:51 , ASP E:67 , HOH E:612 , HOH E:628 , GLU F:82 , HOH F:624
BINDING SITE FOR RESIDUE CD F 201
06
AC6
SOFTWARE
GLU E:82 , HIS F:51 , ASP F:67 , HOH F:683 , HOH F:694
BINDING SITE FOR RESIDUE CD E 201
07
AC7
SOFTWARE
HIS G:51 , HOH G:559 , HOH G:565 , GLU H:82
BINDING SITE FOR RESIDUE CD H 201
08
AC8
SOFTWARE
GLU G:120 , HOH G:573 , HOH G:585
BINDING SITE FOR RESIDUE CD G 202
09
AC9
SOFTWARE
GLU G:82 , HOH G:642 , HIS H:51 , ASP H:67 , HOH H:631 , HOH H:643
BINDING SITE FOR RESIDUE CD G 201
10
BC1
SOFTWARE
HIS I:51 , ASP I:67 , HOH I:697 , HOH I:699 , HOH I:701 , GLU J:82
BINDING SITE FOR RESIDUE CD J 201
11
BC2
SOFTWARE
GLU I:82 , HOH I:677 , HIS J:51 , ASP J:67 , HOH J:660 , HOH J:670
BINDING SITE FOR RESIDUE CD I 201
12
BC3
SOFTWARE
HIS K:51 , ASP K:67 , HOH K:564 , HOH K:586 , GLU L:82 , HOH L:583
BINDING SITE FOR RESIDUE CD L 201
13
BC4
SOFTWARE
GLU K:82 , HIS L:51 , ASP L:67 , HOH L:526 , HOH L:531 , HOH L:540
BINDING SITE FOR RESIDUE CD K 201
14
BC5
SOFTWARE
ASP A:146 , ASP E:146 , ASP I:146
BINDING SITE FOR RESIDUE TRS A 301
15
BC6
SOFTWARE
GLU C:64 , GLU G:64 , GLU K:64 , HOH K:623
BINDING SITE FOR RESIDUE TRS K 302
16
BC7
SOFTWARE
GLU C:167 , GLU G:167 , ALA K:57 , GLU K:167
BINDING SITE FOR RESIDUE TRS C 303
17
BC8
SOFTWARE
ASP B:146 , ASP H:146 , ASP K:146
BINDING SITE FOR RESIDUE TRS B 304
18
BC9
SOFTWARE
GLU D:64 , GLU I:64
BINDING SITE FOR RESIDUE TRS D 305
19
CC1
SOFTWARE
ALA D:57 , GLU D:167 , ALA F:57 , GLU F:167 , ALA I:57 , GLU I:167
BINDING SITE FOR RESIDUE TRS D 306
20
CC2
SOFTWARE
ASP C:146 , ASP F:146 , ASP L:146
BINDING SITE FOR RESIDUE TRS C 307
21
CC3
SOFTWARE
GLU A:64 , GLU H:64 , HOH H:621 , GLU J:64
BINDING SITE FOR RESIDUE TRS H 308
22
CC4
SOFTWARE
GLU A:167 , GLU H:167 , ALA J:57 , GLU J:167
BINDING SITE FOR RESIDUE TRS A 309
23
CC5
SOFTWARE
ASP D:146 , ASP G:146 , ASP J:146
BINDING SITE FOR RESIDUE TRS D 310
24
CC6
SOFTWARE
HOH B:560 , GLU E:64 , GLU L:64
BINDING SITE FOR RESIDUE TRS E 311
25
CC7
SOFTWARE
GLU B:167 , HOH B:518 , GLU E:167 , HOH E:521 , GLU L:167
BINDING SITE FOR RESIDUE TRS B 312
[
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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
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: DPS_1 (A:51-67,B:51-67,C:51-67,D:51-67,E:...)
2: DPS_2 (A:77-91,B:77-91,C:77-91,D:77-91,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_ECOLI
51-67
12
A:51-67
B:51-67
C:51-67
D:51-67
E:51-67
F:51-67
G:51-67
H:51-67
I:51-67
J:51-67
K:51-67
L:51-67
2
DPS_2
PS00819
Dps protein family signature 2.
DPS_ECOLI
77-91
12
A:77-91
B:77-91
C:77-91
D:77-91
E:77-91
F:77-91
G:77-91
H:77-91
I:77-91
J:77-91
K:77-91
L:77-91
[
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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_d1jrea_ (A:)
1b: SCOP_d1jreb_ (B:)
1c: SCOP_d1jrec_ (C:)
1d: SCOP_d1jred_ (D:)
1e: SCOP_d1jree_ (E:)
1f: SCOP_d1jref_ (F:)
1g: SCOP_d1jreg_ (G:)
1h: SCOP_d1jreh_ (H:)
1i: SCOP_d1jrei_ (I:)
1j: SCOP_d1jrej_ (J:)
1k: SCOP_d1jrek_ (K:)
1l: SCOP_d1jrel_ (L:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Escherichia coli, Dps [TaxId: 562]
(7)
1a
d1jrea_
A:
1b
d1jreb_
B:
1c
d1jrec_
C:
1d
d1jred_
D:
1e
d1jree_
E:
1f
d1jref_
F:
1g
d1jreg_
G:
1h
d1jreh_
H:
1i
d1jrei_
I:
1j
d1jrej_
J:
1k
d1jrek_
K:
1l
d1jrel_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1jreA00 (A:11-167)
1b: CATH_1jreB00 (B:11-167)
1c: CATH_1jreK00 (K:13-167)
1d: CATH_1jreL00 (L:13-167)
1e: CATH_1jreD00 (D:11-167)
1f: CATH_1jreH00 (H:11-167)
1g: CATH_1jreE00 (E:12-167)
1h: CATH_1jreF00 (F:12-167)
1i: CATH_1jreI00 (I:12-167)
1j: CATH_1jreC00 (C:13-167)
1k: CATH_1jreG00 (G:13-167)
1l: CATH_1jreJ00 (J:13-167)
View:
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(
)
(
)
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)
(
)
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)
Escherichia coli. Organism_taxid: 562.
(4)
1a
1jreA00
A:11-167
1b
1jreB00
B:11-167
1c
1jreK00
K:13-167
1d
1jreL00
L:13-167
1e
1jreD00
D:11-167
1f
1jreH00
H:11-167
1g
1jreE00
E:12-167
1h
1jreF00
F:12-167
1i
1jreI00
I:12-167
1j
1jreC00
C:13-167
1k
1jreG00
G:13-167
1l
1jreJ00
J:13-167
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_1jreL01 (L:30-167)
1b: PFAM_Ferritin_1jreL02 (L:30-167)
1c: PFAM_Ferritin_1jreL03 (L:30-167)
1d: PFAM_Ferritin_1jreL04 (L:30-167)
1e: PFAM_Ferritin_1jreL05 (L:30-167)
1f: PFAM_Ferritin_1jreL06 (L:30-167)
1g: PFAM_Ferritin_1jreL07 (L:30-167)
1h: PFAM_Ferritin_1jreL08 (L:30-167)
1i: PFAM_Ferritin_1jreL09 (L:30-167)
1j: PFAM_Ferritin_1jreL10 (L:30-167)
1k: PFAM_Ferritin_1jreL11 (L:30-167)
1l: PFAM_Ferritin_1jreL12 (L:30-167)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Escherichia coli (strain K12)
(4)
1a
Ferritin-1jreL01
L:30-167
1b
Ferritin-1jreL02
L:30-167
1c
Ferritin-1jreL03
L:30-167
1d
Ferritin-1jreL04
L:30-167
1e
Ferritin-1jreL05
L:30-167
1f
Ferritin-1jreL06
L:30-167
1g
Ferritin-1jreL07
L:30-167
1h
Ferritin-1jreL08
L:30-167
1i
Ferritin-1jreL09
L:30-167
1j
Ferritin-1jreL10
L:30-167
1k
Ferritin-1jreL11
L:30-167
1l
Ferritin-1jreL12
L:30-167
[
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Asym.Unit (310 KB)
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