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2V08
Biol. Unit 1
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Asym.Unit (38 KB)
Biol.Unit 1 (89 KB)
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(1)
Title
:
STRUCTURE OF WILD-TYPE PHORMIDIUM LAMINOSUM CYTOCHROME C6
Authors
:
J. A. R. Worrall, B. G. Schlarb-Ridley, T. Reda, M. J. Marcaida, R. J. Moorlen, J. Wastl, J. Hirst, D. S. Bendall, B. F. Luisi, C. J. Howe
Date
:
10 May 07 (Deposition) - 24 Jul 07 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Cytochrome, Photosynthesis, Cyano-Bacteria, Electron-Transfer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. R. Worrall, B. G. Schlarb-Ridley, T. Reda, M. J. Marcaida, R. J. Moorlen, J. Wastl, J. Hirst, D. S. Bendall, B. F. Luisi, C. J. Howe
Modulation Of Heme Redox Potential In The Cytochrome C(6) Family
J. Am. Chem. Soc. V. 129 9468 2007
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
3c: IMIDAZOLE (IMDc)
3d: IMIDAZOLE (IMDd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
IMD
12
Ligand/Ion
IMIDAZOLE
4
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:14 , CYS A:15 , CYS A:18 , HIS A:19 , ASN A:24 , VAL A:26 , ASN A:27 , LYS A:30 , THR A:31 , LEU A:32 , PHE A:40 , MET A:42 , GLN A:51 , VAL A:52 , LYS A:56 , ALA A:57 , GLY A:58 , MET A:59 , PRO A:60 , HOH A:2062 , HOH A:2063 , HOH A:2064 , ALA B:17
BINDING SITE FOR RESIDUE HEM A1087
02
AC2
SOFTWARE
ASN A:24 , LEU A:25 , ALA A:28 , ZN A:1091 , HOH A:2018
BINDING SITE FOR RESIDUE IMD A1088
03
AC3
SOFTWARE
GLU A:35 , TYR A:77 , GLN A:81 , TRP A:86 , ZN A:1093 , CL A:1095 , CL A:1096 , CL A:1097
BINDING SITE FOR RESIDUE IMD A1089
04
AC4
SOFTWARE
ASN B:14 , CYS B:15 , CYS B:18 , HIS B:19 , ASN B:24 , ASN B:27 , LYS B:30 , THR B:31 , LEU B:32 , PHE B:40 , MET B:42 , GLN B:51 , LYS B:56 , MET B:59 , PHE B:62 , HOH B:2039 , HOH B:2040
BINDING SITE FOR RESIDUE HEM B1087
05
AC5
SOFTWARE
ASN B:24 , LEU B:25 , ZN B:1090 , HOH B:2013
BINDING SITE FOR RESIDUE IMD B1088
06
AC6
SOFTWARE
GLU B:35 , TYR B:77 , GLN B:81 , TRP B:86 , ZN B:1091
BINDING SITE FOR RESIDUE IMD B1089
07
AC7
SOFTWARE
ASN A:27 , GLU A:29 , HOH A:2065 , HOH A:2066
BINDING SITE FOR RESIDUE ZN A1090
08
AC8
SOFTWARE
IMD A:1088 , HOH A:2067
BINDING SITE FOR RESIDUE ZN A1091
09
AC9
SOFTWARE
IMD B:1088 , HOH B:2041
BINDING SITE FOR RESIDUE ZN B1090
10
BC1
SOFTWARE
IMD B:1089 , HOH B:2042 , HOH B:2043 , HOH B:2044
BINDING SITE FOR RESIDUE ZN B1091
11
BC2
SOFTWARE
ASP A:68 , HOH A:2068
BINDING SITE FOR RESIDUE ZN A1092
12
BC3
SOFTWARE
IMD A:1089 , CL A:1095 , CL A:1096 , CL A:1097
BINDING SITE FOR RESIDUE ZN A1093
13
BC4
SOFTWARE
ASN B:27 , GLU B:29 , HOH B:2045 , HOH B:2046
BINDING SITE FOR RESIDUE ZN B1092
14
BC5
SOFTWARE
GLU B:35 , TRP B:86
BINDING SITE FOR RESIDUE ZN B1093
15
BC6
SOFTWARE
GLU A:35 , TRP A:86 , HOH A:2069
BINDING SITE FOR RESIDUE ZN A1094
16
BC7
SOFTWARE
GLY A:21 , THR A:31 , IMD A:1089 , ZN A:1093
BINDING SITE FOR RESIDUE CL A1095
17
BC8
SOFTWARE
PHE A:11 , GLY A:21 , IMD A:1089 , ZN A:1093 , CL A:1097 , HOH A:2030
BINDING SITE FOR RESIDUE CL A1096
18
BC9
SOFTWARE
GLU A:35 , ALA A:36 , LYS A:39 , IMD A:1089 , ZN A:1093 , CL A:1096
BINDING SITE FOR RESIDUE CL A1097
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
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End label:
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Exons
(0, 0)
Info
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All Exon Boundaries
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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, 2)
Info
All SCOP Domains
1a: SCOP_d2v08a_ (A:)
1b: SCOP_d2v08b_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
automated matches
(20)
Phormidium laminosum [TaxId: 32059]
(2)
1a
d2v08a_
A:
1b
d2v08b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2v08A00 (A:3-86)
1b: CATH_2v08B00 (B:3-86)
View:
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Classes
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Phormidium laminosum. Organism_taxid: 32059.
(1)
1a
2v08A00
A:3-86
1b
2v08B00
B:3-86
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Cytochrome_CBB3_2v08B01 (B:3-78)
1b: PFAM_Cytochrome_CBB3_2v08B02 (B:3-78)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrome_CBB3
(20)
Synechococcus lividus
(1)
1a
Cytochrome_CBB3-2v08B01
B:3-78
1b
Cytochrome_CBB3-2v08B02
B:3-78
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Asymmetric Unit 1
Asymmetric Unit 2
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (38 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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