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3QVD
Asym. Unit
Info
Asym.Unit (234 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (60 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (60 KB)
Biol.Unit 5 (116 KB)
Biol.Unit 6 (116 KB)
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(1)
Title
:
EXPOSURE OF RUBRERYTHRIN FROM PYROCOCCUS FURIOSUS TO PEROXIDE, FIFTEEN SECOND TIME POINT.
Authors
:
B. D. Dillard, J. M. Demick, M. W. W. Adams, W. N. Lanzilotta
Date
:
25 Feb 11 (Deposition) - 22 Jun 11 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: A,B,G,H (1x)
Biol. Unit 6: C,D,E,F (1x)
Keywords
:
Rubrerythrin, Peroxide Reduction, Removal Of Reactive Oxygen Species, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. D. Dillard, J. M. Demick, M. W. Adams, W. N. Lanzilotta
A Cryo-Crystallographic Time Course For Peroxide Reduction By Rubrerythrin From Pyrococcus Furiosus.
J. Biol. Inorg. Chem. V. 16 949 2011
[
close entry info
]
Hetero Components
(3, 32)
Info
All Hetero Components
1a: FE (II) ION (FE2a)
1b: FE (II) ION (FE2b)
1c: FE (II) ION (FE2c)
1d: FE (II) ION (FE2d)
1e: FE (II) ION (FE2e)
1f: FE (II) ION (FE2f)
1g: FE (II) ION (FE2g)
1h: FE (II) ION (FE2h)
1i: FE (II) ION (FE2i)
1j: FE (II) ION (FE2j)
1k: FE (II) ION (FE2k)
1l: FE (II) ION (FE2l)
1m: FE (II) ION (FE2m)
1n: FE (II) ION (FE2n)
1o: FE (II) ION (FE2o)
1p: FE (II) ION (FE2p)
1q: FE (II) ION (FE2q)
1r: FE (II) ION (FE2r)
1s: FE (II) ION (FE2s)
1t: FE (II) ION (FE2t)
1u: FE (II) ION (FE2u)
1v: FE (II) ION (FE2v)
1w: FE (II) ION (FE2w)
1x: FE (II) ION (FE2x)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
3a: HYDROGEN PEROXIDE (PEOa)
3b: HYDROGEN PEROXIDE (PEOb)
3c: HYDROGEN PEROXIDE (PEOc)
3d: HYDROGEN PEROXIDE (PEOd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
2
FE
4
Ligand/Ion
FE (III) ION
1
FE2
24
Ligand/Ion
FE (II) ION
3
PEO
4
Ligand/Ion
HYDROGEN PEROXIDE
[
close Hetero Component info
]
Sites
(32, 32)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:80 , GLU A:83 , GLU A:114 , FE2 A:173 , GLU B:19 , GLU B:52 , FE2 B:173
BINDING SITE FOR RESIDUE PEO A 1
02
AC2
SOFTWARE
CYS A:142 , CYS A:145 , CYS A:157 , CYS A:160
BINDING SITE FOR RESIDUE FE2 A 172
03
AC3
SOFTWARE
PEO A:1 , GLU A:80 , GLU A:114 , HIS A:117 , GLU B:52 , FE2 B:173
BINDING SITE FOR RESIDUE FE2 A 173
04
AC4
SOFTWARE
GLU A:19 , GLU A:52 , HIS A:55 , FE A:175 , GLU B:114
BINDING SITE FOR RESIDUE FE2 A 174
05
AC5
SOFTWARE
GLU A:19 , GLU A:52 , FE2 A:174 , GLU B:83 , GLU B:114 , FE2 B:174 , HOH B:204
BINDING SITE FOR RESIDUE FE A 175
06
AC6
SOFTWARE
CYS B:142 , CYS B:145 , CYS B:157 , CYS B:160
BINDING SITE FOR RESIDUE FE2 B 172
07
AC7
SOFTWARE
PEO A:1 , GLU A:114 , FE2 A:173 , GLU B:19 , GLU B:52 , HIS B:55
BINDING SITE FOR RESIDUE FE2 B 173
08
AC8
SOFTWARE
GLU A:52 , FE A:175 , GLU B:80 , GLU B:114 , HIS B:117 , HOH B:204
BINDING SITE FOR RESIDUE FE2 B 174
09
AC9
SOFTWARE
GLU C:80 , GLU C:83 , GLU C:114 , FE2 C:175 , GLU D:19 , GLU D:52 , FE2 D:173
BINDING SITE FOR RESIDUE PEO C 172
10
BC1
SOFTWARE
CYS C:142 , CYS C:145 , CYS C:157 , CYS C:160
BINDING SITE FOR RESIDUE FE2 C 173
11
BC2
SOFTWARE
GLU C:19 , GLU C:52 , HIS C:55 , GLU D:114 , FE D:175
BINDING SITE FOR RESIDUE FE2 C 174
12
BC3
SOFTWARE
GLU C:80 , GLU C:114 , HIS C:117 , PEO C:172 , GLU D:52
BINDING SITE FOR RESIDUE FE2 C 175
13
BC4
SOFTWARE
CYS D:142 , CYS D:145 , CYS D:157 , CYS D:160
BINDING SITE FOR RESIDUE FE2 D 172
14
BC5
SOFTWARE
GLU C:114 , PEO C:172 , GLU D:19 , GLU D:52 , HIS D:55
BINDING SITE FOR RESIDUE FE2 D 173
15
BC6
SOFTWARE
GLU C:52 , GLU D:80 , GLU D:114 , HIS D:117 , FE D:175 , HOH D:197
BINDING SITE FOR RESIDUE FE2 D 174
16
BC7
SOFTWARE
GLU C:19 , GLU C:52 , FE2 C:174 , GLU D:83 , GLU D:114 , FE2 D:174 , HOH D:197
BINDING SITE FOR RESIDUE FE D 175
17
BC8
SOFTWARE
GLU E:80 , GLU E:83 , GLU E:114 , FE2 E:175 , GLU F:19 , GLU F:52 , FE2 F:173
BINDING SITE FOR RESIDUE PEO E 172
18
BC9
SOFTWARE
CYS E:142 , CYS E:145 , CYS E:157 , CYS E:160
BINDING SITE FOR RESIDUE FE2 E 173
19
CC1
SOFTWARE
GLU E:19 , GLU E:52 , HIS E:55 , GLU F:114 , FE2 F:174 , FE F:175
BINDING SITE FOR RESIDUE FE2 E 174
20
CC2
SOFTWARE
GLU E:80 , GLU E:114 , HIS E:117 , PEO E:172 , GLU F:52
BINDING SITE FOR RESIDUE FE2 E 175
21
CC3
SOFTWARE
CYS F:142 , CYS F:145 , CYS F:157 , CYS F:160
BINDING SITE FOR RESIDUE FE2 F 172
22
CC4
SOFTWARE
GLU E:114 , PEO E:172 , GLU F:19 , GLU F:52 , HIS F:55
BINDING SITE FOR RESIDUE FE2 F 173
23
CC5
SOFTWARE
GLU E:52 , FE2 E:174 , GLU F:80 , GLU F:114 , HIS F:117 , FE F:175 , HOH F:205
BINDING SITE FOR RESIDUE FE2 F 174
24
CC6
SOFTWARE
GLU E:19 , GLU E:52 , FE2 E:174 , GLU F:83 , GLU F:114 , FE2 F:174 , HOH F:205
BINDING SITE FOR RESIDUE FE F 175
25
CC7
SOFTWARE
GLU G:80 , GLU G:83 , GLU G:114 , FE2 G:174 , GLU H:19 , GLU H:52 , FE2 H:173
BINDING SITE FOR RESIDUE PEO G 172
26
CC8
SOFTWARE
CYS G:142 , CYS G:145 , CYS G:157 , CYS G:160
BINDING SITE FOR RESIDUE FE2 G 173
27
CC9
SOFTWARE
GLU G:80 , GLU G:114 , HIS G:117 , PEO G:172 , GLU H:52
BINDING SITE FOR RESIDUE FE2 G 174
28
DC1
SOFTWARE
GLU G:19 , GLU G:52 , HIS G:55 , FE G:176 , GLU H:114
BINDING SITE FOR RESIDUE FE2 G 175
29
DC2
SOFTWARE
GLU G:19 , GLU G:52 , FE2 G:175 , GLU H:83 , GLU H:114 , FE2 H:174 , HOH H:196
BINDING SITE FOR RESIDUE FE G 176
30
DC3
SOFTWARE
CYS H:142 , CYS H:145 , CYS H:157 , CYS H:160
BINDING SITE FOR RESIDUE FE2 H 172
31
DC4
SOFTWARE
GLU G:114 , PEO G:172 , GLU H:19 , GLU H:52 , HIS H:55
BINDING SITE FOR RESIDUE FE2 H 173
32
DC5
SOFTWARE
GLU G:52 , FE G:176 , GLU H:80 , GLU H:114 , HIS H:117 , HOH H:196
BINDING SITE FOR RESIDUE FE2 H 174
[
close Site info
]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d3qvda1 (A:2-134)
1b: SCOP_d3qvdg1 (G:2-134)
1c: SCOP_d3qvdh1 (H:2-134)
1d: SCOP_d3qvdb1 (B:2-134)
1e: SCOP_d3qvdc1 (C:2-134)
1f: SCOP_d3qvdd1 (D:2-134)
1g: SCOP_d3qvde1 (E:2-134)
1h: SCOP_d3qvdf1 (F:2-134)
2a: SCOP_d3qvda2 (A:135-171)
2b: SCOP_d3qvdg2 (G:135-171)
2c: SCOP_d3qvdh2 (H:135-171)
2d: SCOP_d3qvdb2 (B:135-171)
2e: SCOP_d3qvdc2 (C:135-171)
2f: SCOP_d3qvdd2 (D:135-171)
2g: SCOP_d3qvde2 (E:135-171)
2h: SCOP_d3qvdf2 (F:135-171)
View:
Select:
Label:
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
:
automated matches
(70)
Pyrococcus furiosus [TaxId: 2261]
(4)
1a
d3qvda1
A:2-134
1b
d3qvdg1
G:2-134
1c
d3qvdh1
H:2-134
1d
d3qvdb1
B:2-134
1e
d3qvdc1
C:2-134
1f
d3qvdd1
D:2-134
1g
d3qvde1
E:2-134
1h
d3qvdf1
F:2-134
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Rubredoxin-like
(127)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Pyrococcus furiosus [TaxId: 2261]
(4)
2a
d3qvda2
A:135-171
2b
d3qvdg2
G:135-171
2c
d3qvdh2
H:135-171
2d
d3qvdb2
B:135-171
2e
d3qvdc2
C:135-171
2f
d3qvdd2
D:135-171
2g
d3qvde2
E:135-171
2h
d3qvdf2
F:135-171
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Rubrerythrin_3qvdH01 (H:10-125)
1b: PFAM_Rubrerythrin_3qvdH02 (H:10-125)
1c: PFAM_Rubrerythrin_3qvdH03 (H:10-125)
1d: PFAM_Rubrerythrin_3qvdH04 (H:10-125)
1e: PFAM_Rubrerythrin_3qvdH05 (H:10-125)
1f: PFAM_Rubrerythrin_3qvdH06 (H:10-125)
1g: PFAM_Rubrerythrin_3qvdH07 (H:10-125)
1h: PFAM_Rubrerythrin_3qvdH08 (H:10-125)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Rubrerythrin
(18)
Pyrococcus furiosus
(5)
1a
Rubrerythrin-3qvdH01
H:10-125
1b
Rubrerythrin-3qvdH02
H:10-125
1c
Rubrerythrin-3qvdH03
H:10-125
1d
Rubrerythrin-3qvdH04
H:10-125
1e
Rubrerythrin-3qvdH05
H:10-125
1f
Rubrerythrin-3qvdH06
H:10-125
1g
Rubrerythrin-3qvdH07
H:10-125
1h
Rubrerythrin-3qvdH08
H:10-125
[
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]
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Asym.Unit (234 KB)
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