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2QJP
Biol. Unit 2
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Asym.Unit (585 KB)
Biol.Unit 1 (289 KB)
Biol.Unit 2 (289 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF WILD TYPE RHODOBACTER SPHAEROIDES WITH STIGMATELLIN AND ANTIMYCIN INHIBITED
Authors
:
L. Esser, D. Xia
Date
:
08 Jul 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Cytochrome B With 8 Tm Helices, One C-Term Tm In Cytochrome C1 And An N-Term Tm In The Iron-Sulfur-Protein (Rieske), Electron Transport, Heme, Membrane, Metal-Binding, Respiratory Chain, Transmembrane, Transport, 2Fe-2S, Inner Membrane, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Esser, M. Elberry, F. Zhou, C. A. Yu, L. Yu, D. Xia
Inhibitor-Complexed Structures Of The Cytochrome Bc1 From The Photosynthetic Bacterium Rhodobacter Sphaeroides.
J. Biol. Chem. V. 283 2846 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 16)
Info
All Hetero Components
1a: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJa)
1b: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJb)
1c: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJc)
1d: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJd)
2a: B-2-OCTYLGLUCOSIDE (BGLa)
2b: B-2-OCTYLGLUCOSIDE (BGLb)
2c: B-2-OCTYLGLUCOSIDE (BGLc)
2d: B-2-OCTYLGLUCOSIDE (BGLd)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
4d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
4f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
4g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
4h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
4i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
4j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
4k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
4l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
5a: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPa)
5b: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPb)
5c: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPc)
5d: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPd)
6a: STIGMATELLIN A (SMAa)
6b: STIGMATELLIN A (SMAb)
6c: STIGMATELLIN A (SMAc)
6d: STIGMATELLIN A (SMAd)
7a: STRONTIUM ION (SRa)
7b: STRONTIUM ION (SRb)
7c: STRONTIUM ION (SRc)
7d: STRONTIUM ION (SRd)
7e: STRONTIUM ION (SRe)
7f: STRONTIUM ION (SRf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANJ
2
Ligand/Ion
(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE
2
BGL
2
Ligand/Ion
B-2-OCTYLGLUCOSIDE
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
LOP
2
Ligand/Ion
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
6
SMA
2
Ligand/Ion
STIGMATELLIN A
7
SR
-1
Ligand/Ion
STRONTIUM ION
[
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Sites
(19, 19)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC9 (SOFTWARE)
19: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
VAL G:262 , PHE G:269 , HOH G:506 , GLU H:14 , GLY H:15 , GLY H:124 , LYS H:227
BINDING SITE FOR RESIDUE BGL G 431
02
AC4
SOFTWARE
ALA J:265 , PHE J:269 , GLY K:15 , PHE K:122 , ASN K:123 , GLY K:124
BINDING SITE FOR RESIDUE BGL J 431
03
AC7
SOFTWARE
ASP H:8 , VAL H:9 , GLU H:14 , GLU H:129
BINDING SITE FOR RESIDUE SR H 257
04
AC8
SOFTWARE
ASP K:8 , VAL K:9 , GLU K:14 , GLU K:129
BINDING SITE FOR RESIDUE SR K 257
05
AC9
SOFTWARE
ASP A:311 , ASP J:311
BINDING SITE FOR RESIDUE SR J 432
06
BC9
SOFTWARE
TRP G:45 , GLY G:48 , LEU G:51 , HIS G:111 , ARG G:114 , SER G:120 , ARG G:125 , TRP G:129 , GLY G:132 , MET G:133 , ILE G:135 , VAL G:209 , HIS G:212 , PHE G:216 , GLY G:220 , ASN G:221 , ASN G:222 , ANJ G:505 , HOH G:525
BINDING SITE FOR RESIDUE HEM G 501
07
CC1
SOFTWARE
GLN G:58 , GLY G:62 , ILE G:63 , ARG G:94 , HIS G:97 , THR G:142 , GLY G:146 , TYR G:147 , LEU G:149 , PRO G:150 , HIS G:198 , TYR G:199 , PRO G:202
BINDING SITE FOR RESIDUE HEM G 502
08
CC2
SOFTWARE
VAL H:35 , CYS H:36 , CYS H:39 , HIS H:40 , LEU H:94 , ASN H:96 , PRO H:98 , MET H:103 , ARG H:107 , TYR H:130 , ILE H:183 , ALA H:184 , MET H:185
BINDING SITE FOR RESIDUE HEM H 301
09
CC3
SOFTWARE
CYS I:129 , HIS I:131 , LEU I:132 , CYS I:149 , HIS I:152 , SER I:154
BINDING SITE FOR RESIDUE FES I 200
10
CC4
SOFTWARE
TRP J:45 , GLY J:48 , LEU J:51 , VAL J:108 , HIS J:111 , ARG J:114 , SER J:120 , ARG J:125 , THR J:128 , TRP J:129 , GLY J:132 , MET J:133 , ILE J:135 , VAL J:209 , HIS J:212 , PHE J:216 , THR J:219 , GLY J:220 , ASN J:221 , ASN J:222 , ANJ J:505
BINDING SITE FOR RESIDUE HEM J 501
11
CC5
SOFTWARE
GLN J:58 , GLY J:62 , ILE J:63 , ALA J:66 , ARG J:94 , HIS J:97 , THR J:142 , GLY J:146 , TYR J:147 , LEU J:149 , PRO J:150 , HIS J:198 , TYR J:199 , PRO J:202
BINDING SITE FOR RESIDUE HEM J 502
12
CC6
SOFTWARE
VAL K:35 , CYS K:36 , CYS K:39 , HIS K:40 , LEU K:94 , ASN K:96 , PRO K:98 , MET K:103 , ARG K:107 , TYR K:130 , LEU K:135 , ILE K:183 , ALA K:184 , MET K:185
BINDING SITE FOR RESIDUE HEM K 301
13
CC7
SOFTWARE
CYS L:129 , HIS L:131 , LEU L:132 , GLY L:133 , CYS L:149 , HIS L:152 , SER L:154
BINDING SITE FOR RESIDUE FES L 200
14
DC1
SOFTWARE
PHE G:144 , MET G:154 , GLY G:158 , VAL G:161 , ILE G:162 , LEU G:180 , LEU G:197 , ILE G:292 , GLU G:295 , PHE G:298 , TYR G:302 , MET G:336 , PHE G:337 , ILE G:340 , CYS L:151 , HIS L:152
BINDING SITE FOR RESIDUE SMA G 503
15
DC2
SOFTWARE
CYS I:151 , HIS I:152 , PHE J:144 , GLY J:158 , VAL J:161 , PHE J:194 , ILE J:292 , PRO J:294 , GLU J:295 , PHE J:298 , TYR J:302 , MET J:336 , PHE J:337 , ILE J:340
BINDING SITE FOR RESIDUE SMA J 503
16
DC3
SOFTWARE
MET J:44 , LEU J:103 , PHE J:113 , TYR J:117 , TYR J:118 , PHE J:263 , LEU J:274 , TRP J:296 , ARG J:358 , TRP J:368
BINDING SITE FOR RESIDUE LOP J 504
17
DC6
SOFTWARE
MET G:44 , LEU G:103 , PHE G:113 , TYR G:117 , TYR G:118 , PHE G:263 , LEU G:274 , ARG G:358 , PHE G:367 , TRP G:368 , PHE G:374
BINDING SITE FOR RESIDUE LOP G 504
18
DC9
SOFTWARE
ALA G:29 , THR G:32 , LEU G:41 , TRP G:45 , VAL G:49 , ALA G:52 , VAL G:209 , ILE G:213 , PHE G:216 , PHE G:244 , PHE G:248 , ASP G:252 , HEM G:501
BINDING SITE FOR RESIDUE ANJ G 505
19
EC1
SOFTWARE
ALA J:29 , LEU J:41 , TRP J:45 , ILE J:46 , VAL J:49 , ALA J:52 , VAL J:209 , ILE J:213 , PHE J:216 , PHE J:244 , PHE J:248 , ASP J:252 , HEM J:501
BINDING SITE FOR RESIDUE ANJ J 505
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (G:15-225,J:15-225)
2: CYTC (H:23-142,K:23-142)
3: RIESKE (I:117-185,L:117-185)
4: CYTB_CTER (G:234-422,J:234-422)
;
View:
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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_RHOSH
15-225
2
-
-
G:15-225
J:15-225
2
CYTC
PS51007
Cytochrome c family profile.
CY1_RHOSH
45-164
2
-
-
H:23-142
K:23-142
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_RHOSH
117-185
2
-
-
I:117-185
L:117-185
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_RHOSH
234-422
2
-
-
G:234-422
J:234-422
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
(0, 0)
Info
All SCOP Domains
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Label:
Sorry, no Info available
[
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CATH Domains
(5, 20)
Info
all CATH domains
1a: CATH_2qjpB01 (B:1-221)
1b: CATH_2qjpE01 (E:1-221)
1c: CATH_2qjpH01 (H:1-221)
1d: CATH_2qjpK01 (K:1-221)
2a: CATH_2qjpA00 (A:3-430)
2b: CATH_2qjpD00 (D:3-430)
2c: CATH_2qjpG00 (G:3-430)
2d: CATH_2qjpJ00 (J:3-430)
3a: CATH_2qjpB02 (B:222-256)
3b: CATH_2qjpE02 (E:222-256)
3c: CATH_2qjpH02 (H:222-256)
3d: CATH_2qjpK02 (K:222-256)
4a: CATH_2qjpC01 (C:9-41)
4b: CATH_2qjpF01 (F:9-41)
4c: CATH_2qjpI01 (I:9-41)
4d: CATH_2qjpL01 (L:9-41)
5a: CATH_2qjpC02 (C:42-187)
5b: CATH_2qjpF02 (F:42-187)
5c: CATH_2qjpI02 (I:42-187)
5d: CATH_2qjpL02 (L:42-187)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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 sphaeroides. Organism_taxid: 1063.
(4)
1a
2qjpB01
B:1-221
1b
2qjpE01
E:1-221
1c
2qjpH01
H:1-221
1d
2qjpK01
K:1-221
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
2a
2qjpA00
A:3-430
2b
2qjpD00
D:3-430
2c
2qjpG00
G:3-430
2d
2qjpJ00
J:3-430
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 sphaeroides. Organism_taxid: 1063.
(4)
3a
2qjpB02
B:222-256
3b
2qjpE02
E:222-256
3c
2qjpH02
H:222-256
3d
2qjpK02
K:222-256
Homologous Superfamily
:
Single helix bin
(16)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
4a
2qjpC01
C:9-41
4b
2qjpF01
F:9-41
4c
2qjpI01
I:9-41
4d
2qjpL01
L:9-41
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(10)
5a
2qjpC02
C:42-187
5b
2qjpF02
F:42-187
5c
2qjpI02
I:42-187
5d
2qjpL02
L:42-187
[
close CATH info
]
Pfam Domains
(5, 20)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_2qjpJ01 (J:102-277)
1b: PFAM_Cytochrom_B_N_2_2qjpJ02 (J:102-277)
1c: PFAM_Cytochrom_B_N_2_2qjpJ03 (J:102-277)
1d: PFAM_Cytochrom_B_N_2_2qjpJ04 (J:102-277)
2a: PFAM_Cytochrom_C1_2qjpK01 (K:11-255)
2b: PFAM_Cytochrom_C1_2qjpK02 (K:11-255)
2c: PFAM_Cytochrom_C1_2qjpK03 (K:11-255)
2d: PFAM_Cytochrom_C1_2qjpK04 (K:11-255)
3a: PFAM_Rieske_2qjpL01 (L:95-180)
3b: PFAM_Rieske_2qjpL02 (L:95-180)
3c: PFAM_Rieske_2qjpL03 (L:95-180)
3d: PFAM_Rieske_2qjpL04 (L:95-180)
4a: PFAM_UCR_Fe_S_N_2qjpL05 (L:9-41)
4b: PFAM_UCR_Fe_S_N_2qjpL06 (L:9-41)
4c: PFAM_UCR_Fe_S_N_2qjpL07 (L:9-41)
4d: PFAM_UCR_Fe_S_N_2qjpL08 (L:9-41)
5a: PFAM_Cytochrom_B_C_2qjpJ05 (J:282-416)
5b: PFAM_Cytochrom_B_C_2qjpJ06 (J:282-416)
5c: PFAM_Cytochrom_B_C_2qjpJ07 (J:282-416)
5d: PFAM_Cytochrom_B_C_2qjpJ08 (J:282-416)
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Clans
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(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
1a
Cytochrom_B_N_2-2qjpJ01
J:102-277
1b
Cytochrom_B_N_2-2qjpJ02
J:102-277
1c
Cytochrom_B_N_2-2qjpJ03
J:102-277
1d
Cytochrom_B_N_2-2qjpJ04
J:102-277
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
2a
Cytochrom_C1-2qjpK01
K:11-255
2b
Cytochrom_C1-2qjpK02
K:11-255
2c
Cytochrom_C1-2qjpK03
K:11-255
2d
Cytochrom_C1-2qjpK04
K:11-255
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(8)
3a
Rieske-2qjpL01
L:95-180
3b
Rieske-2qjpL02
L:95-180
3c
Rieske-2qjpL03
L:95-180
3d
Rieske-2qjpL04
L:95-180
Clan
:
TAT
(4)
Family
:
UCR_Fe-S_N
(4)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
4a
UCR_Fe-S_N-2qjpL05
L:9-41
4b
UCR_Fe-S_N-2qjpL06
L:9-41
4c
UCR_Fe-S_N-2qjpL07
L:9-41
4d
UCR_Fe-S_N-2qjpL08
L:9-41
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
5a
Cytochrom_B_C-2qjpJ05
J:282-416
5b
Cytochrom_B_C-2qjpJ06
J:282-416
5c
Cytochrom_B_C-2qjpJ07
J:282-416
5d
Cytochrom_B_C-2qjpJ08
J:282-416
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