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1ZRT
Asym. Unit
Info
Asym.Unit (290 KB)
Biol.Unit 1 (275 KB)
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(1)
Title
:
RHODOBACTER CAPSULATUS CYTOCHROME BC1 COMPLEX WITH STIGMATELLIN BOUND
Authors
:
E. A. Berry, L. S. Huang, L. K. Saechao, N. G. Pon, M. Valkova-Valchanov, F. Daldal
Date
:
22 May 05 (Deposition) - 07 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : C,D,E,P,Q,R
Biol. Unit 1: C,D,E,P,Q,R (1x)
Keywords
:
Cytochrome Bc1, Membrane Protein, Heme Protein, Rieske Iron Sulfur Protein, Cytochrome B, Cytochrome C1, Complex Iii, Oxidoreductase, Redox Enzyme, Respiratory Chain, Stigmatellin, Oxidoreductase/Metal Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. A. Berry, L. S. Huang, L. K. Saechao, N. G. Pon, M. Valkova-Valchanova, F. Daldal
X-Ray Structure Of Rhodobacter Capsulatus Cytochrome Bc (1): Comparison With Its Mitochondrial And Chloroplast Counterparts.
Photosynth. Res. V. 81 251 2004
(for further references see the
PDB file header
)
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
1b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2a: HEME C (HECa)
2b: HEME C (HECb)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4a: STIGMATELLIN A (SMAa)
4b: STIGMATELLIN A (SMAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
HEC
2
Ligand/Ion
HEME C
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
SMA
2
Ligand/Ion
STIGMATELLIN A
[
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN C:58 , GLY C:62 , ILE C:63 , LEU C:65 , ALA C:66 , TYR C:69 , ARG C:94 , HIS C:97 , ALA C:143 , GLY C:146 , TYR C:147 , HIS C:198 , PRO C:202 , TYR C:297
BINDING SITE FOR RESIDUE HEM C 501
02
AC2
SOFTWARE
TRP C:45 , ILE C:46 , TRP C:47 , GLY C:48 , ILE C:49 , LEU C:51 , ALA C:52 , HIS C:111 , ILE C:112 , ARG C:114 , GLY C:132 , ILE C:135 , MET C:139 , VAL C:209 , HIS C:212 , PHE C:216 , ASN C:221 , ASN C:222
BINDING SITE FOR RESIDUE HEM C 502
03
AC3
SOFTWARE
LEU C:137 , MET C:140 , PHE C:144 , MET C:154 , GLY C:158 , VAL C:161 , ILE C:162 , PHE C:166 , LEU C:180 , PHE C:194 , PRO C:294 , GLU C:295 , PHE C:298 , PHE C:301 , TYR C:302 , MET C:336 , PHE C:337 , HIS R:156
BINDING SITE FOR RESIDUE SMA C 503
04
AC4
SOFTWARE
VAL D:33 , CYS D:34 , CYS D:37 , HIS D:38 , MET D:96 , GLY D:97 , LEU D:100 , MET D:103 , ARG D:107 , TYR D:130 , TYR D:134 , VAL D:135 , PHE D:158 , ALA D:181 , ARG D:182 , MET D:183 , PRO D:184
BINDING SITE FOR RESIDUE HEC D 501
05
AC5
SOFTWARE
CYS E:133 , HIS E:135 , LEU E:136 , CYS E:138 , CYS E:153 , CYS E:155 , HIS E:156 , SER E:158
BINDING SITE FOR RESIDUE FES E 501
06
AC6
SOFTWARE
GLN P:58 , GLY P:62 , ILE P:63 , LEU P:65 , ALA P:66 , TYR P:69 , ARG P:94 , HIS P:97 , ALA P:143 , GLY P:146 , TYR P:147 , HIS P:198 , PRO P:202 , TYR P:297
BINDING SITE FOR RESIDUE HEM P 501
07
AC7
SOFTWARE
TRP P:45 , ILE P:46 , TRP P:47 , GLY P:48 , ILE P:49 , LEU P:51 , ALA P:52 , HIS P:111 , ILE P:112 , ARG P:114 , GLY P:132 , ILE P:135 , MET P:139 , VAL P:209 , HIS P:212 , PHE P:216 , ASN P:221 , ASN P:222
BINDING SITE FOR RESIDUE HEM P 502
08
AC8
SOFTWARE
HIS E:156 , LEU P:137 , MET P:140 , PHE P:144 , MET P:154 , GLY P:158 , VAL P:161 , ILE P:162 , PHE P:166 , LEU P:180 , PHE P:194 , PRO P:294 , GLU P:295 , PHE P:298 , PHE P:301 , TYR P:302 , MET P:336 , PHE P:337
BINDING SITE FOR RESIDUE SMA P 503
09
AC9
SOFTWARE
VAL Q:33 , CYS Q:34 , CYS Q:37 , HIS Q:38 , MET Q:96 , GLY Q:97 , LEU Q:100 , MET Q:103 , ARG Q:107 , TYR Q:130 , TYR Q:134 , VAL Q:135 , PHE Q:158 , ALA Q:181 , ARG Q:182 , MET Q:183 , PRO Q:184
BINDING SITE FOR RESIDUE HEC Q 501
10
BC1
SOFTWARE
CYS R:133 , HIS R:135 , LEU R:136 , CYS R:138 , CYS R:153 , CYS R:155 , HIS R:156 , SER R:158
BINDING SITE FOR RESIDUE FES R 501
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 12)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (C:15-225,P:15-225,C:15-225,P:15-22...)
2: CYTC (D:21-199,Q:21-199,D:21-142,Q:21-14...)
3: RIESKE (E:94-189,R:94-189,E:124-189,R:124-...)
4: CYTB_CTER (C:234-422,P:234-422,C:234-422,P:23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_NTER
PS51002
Cytochrome b/b6 N-terminal region profile.
CYB_RHOCA
15-225
2
C:15-225
P:15-225
CYB_RHOCB
15-225
2
C:15-225
P:15-225
2
CYTC
PS51007
Cytochrome c family profile.
CY1_RHOCA
42-221
2
D:21-199
Q:21-199
CY1_RHOCB
42-163
2
D:21-142
Q:21-142
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_RHOCB
94-189
2
E:94-189
R:94-189
UCRI_RHOCA
124-189
2
E:124-189
R:124-189
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_RHOCA
234-422
2
C:234-422
P:234-422
CYB_RHOCB
234-422
2
C:234-422
P:234-422
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_1zrtD01 (D:2-219)
1b: CATH_1zrtQ01 (Q:2-219)
2a: CATH_1zrtC00 (C:2-428)
2b: CATH_1zrtP00 (P:2-428)
3a: CATH_1zrtD02 (D:220-258)
3b: CATH_1zrtQ02 (Q:220-258)
4a: CATH_1zrtE01 (E:11-41)
4b: CATH_1zrtR01 (R:11-41)
5a: CATH_1zrtE02 (E:42-191)
5b: CATH_1zrtR02 (R:42-191)
View:
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)
(
)
Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter capsulatus. Organism_taxid: 1061.
(3)
1a
1zrtD01
D:2-219
1b
1zrtQ01
Q:2-219
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Rhodobacter capsulatus. Organism_taxid: 1061.
(1)
2a
1zrtC00
C:2-428
2b
1zrtP00
P:2-428
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.100, no name defined]
(56)
Rhodobacter capsulatus. Organism_taxid: 1061.
(1)
3a
1zrtD02
D:220-258
3b
1zrtQ02
Q:220-258
Homologous Superfamily
:
Single helix bin
(16)
Rhodobacter capsulatus. Organism_taxid: 1061.
(1)
4a
1zrtE01
E:11-41
4b
1zrtR01
R:11-41
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Rhodobacter capsulatus. Organism_taxid: 1061.
(1)
5a
1zrtE02
E:42-191
5b
1zrtR02
R:42-191
[
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]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_1zrtP01 (P:102-279)
1b: PFAM_Cytochrom_B_N_2_1zrtP02 (P:102-279)
2a: PFAM_Cytochrom_C1_1zrtQ01 (Q:9-252)
2b: PFAM_Cytochrom_C1_1zrtQ02 (Q:9-252)
3a: PFAM_Rieske_1zrtR01 (R:91-185)
3b: PFAM_Rieske_1zrtR02 (R:91-185)
4a: PFAM_UCR_Fe_S_N_1zrtR03 (R:11-41)
4b: PFAM_UCR_Fe_S_N_1zrtR04 (R:11-41)
5a: PFAM_Cytochrom_B_C_1zrtP03 (P:282-404)
5b: PFAM_Cytochrom_B_C_1zrtP04 (P:282-404)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(1)
1a
Cytochrom_B_N_2-1zrtP01
P:102-279
1b
Cytochrom_B_N_2-1zrtP02
P:102-279
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(1)
2a
Cytochrom_C1-1zrtQ01
Q:9-252
2b
Cytochrom_C1-1zrtQ02
Q:9-252
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(1)
3a
Rieske-1zrtR01
R:91-185
3b
Rieske-1zrtR02
R:91-185
Clan
:
TAT
(4)
Family
:
UCR_Fe-S_N
(4)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(1)
4a
UCR_Fe-S_N-1zrtR03
R:11-41
4b
UCR_Fe-S_N-1zrtR04
R:11-41
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(1)
5a
Cytochrom_B_C-1zrtP03
P:282-404
5b
Cytochrom_B_C-1zrtP04
P:282-404
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