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2QJK
Biol. Unit 2
Info
Asym.Unit (876 KB)
Biol.Unit 1 (293 KB)
Biol.Unit 2 (294 KB)
Biol.Unit 3 (294 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF MUTANT RHODOBACTER SPHAEROIDES BC1 WITH STIGMATELLIN AND ANTIMYCIN
Authors
:
L. Esser
Date
:
07 Jul 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Keywords
:
Cytochrome B, Tm Helices, Cytochrome C1, C-Terminal Tm Helix, Iron-Sulfur-Protein, N-Terminal Tm, 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)
1e: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJe)
1f: (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMIN... (ANJf)
2a: B-2-OCTYLGLUCOSIDE (BGLa)
2b: B-2-OCTYLGLUCOSIDE (BGLb)
2c: B-2-OCTYLGLUCOSIDE (BGLc)
2d: B-2-OCTYLGLUCOSIDE (BGLd)
2e: B-2-OCTYLGLUCOSIDE (BGLe)
2f: B-2-OCTYLGLUCOSIDE (BGLf)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3e: FE2/S2 (INORGANIC) CLUSTER (FESe)
3f: FE2/S2 (INORGANIC) CLUSTER (FESf)
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)
4m: PROTOPORPHYRIN IX CONTAINING FE (HEMm)
4n: PROTOPORPHYRIN IX CONTAINING FE (HEMn)
4o: PROTOPORPHYRIN IX CONTAINING FE (HEMo)
4p: PROTOPORPHYRIN IX CONTAINING FE (HEMp)
4q: PROTOPORPHYRIN IX CONTAINING FE (HEMq)
4r: PROTOPORPHYRIN IX CONTAINING FE (HEMr)
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)
5e: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPe)
5f: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPf)
6a: STIGMATELLIN A (SMAa)
6b: STIGMATELLIN A (SMAb)
6c: STIGMATELLIN A (SMAc)
6d: STIGMATELLIN A (SMAd)
6e: STIGMATELLIN A (SMAe)
6f: STIGMATELLIN A (SMAf)
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
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC1 (SOFTWARE)
13: EC3 (SOFTWARE)
14: EC4 (SOFTWARE)
15: EC9 (SOFTWARE)
16: FC1 (SOFTWARE)
17: FC6 (SOFTWARE)
18: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
PHE G:269 , GLU H:14 , LYS H:227
BINDING SITE FOR RESIDUE BGL G 431
02
AC4
SOFTWARE
PHE J:269 , GLY K:124 , LYS K:227
BINDING SITE FOR RESIDUE BGL J 431
03
AC9
SOFTWARE
ASP H:8 , VAL H:9 , GLU H:14 , GLU H:129
BINDING SITE FOR RESIDUE SR H 257
04
BC1
SOFTWARE
ASP K:8 , VAL K:9 , GLU K:14
BINDING SITE FOR RESIDUE SR K 257
05
CC3
SOFTWARE
TRP G:45 , GLY G:48 , LEU G:51 , ALA G:52 , HIS G:111 , ILE G:112 , ARG G:114 , ARG G:125 , TRP G:129 , GLY G:132 , MET G:133 , ILE G:135 , TYR G:136 , VAL G:209 , HIS G:212 , PHE G:216 , ASN G:222 , ANJ G:505
BINDING SITE FOR RESIDUE HEM G 501
06
CC4
SOFTWARE
GLN G:58 , GLY G:62 , ILE G:63 , VAL G:80 , ARG G:94 , HIS G:97 , ALA G:98 , PHE G:104 , GLY G:146 , LEU G:149 , PRO G:150 , HIS G:198 , TYR G:199 , PRO G:202
BINDING SITE FOR RESIDUE HEM G 502
07
CC5
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 , LEU H:135 , ILE H:183 , ALA H:184 , MET H:185
BINDING SITE FOR RESIDUE HEM H 301
08
CC6
SOFTWARE
CYS I:129 , HIS I:131 , LEU I:132 , GLY I:133 , CYS I:149 , HIS I:152 , SER I:154
BINDING SITE FOR RESIDUE FES I 200
09
CC7
SOFTWARE
TRP J:45 , GLY J:48 , LEU J:51 , ALA J:52 , HIS J:111 , ARG J:114 , ARG J:125 , TRP J:129 , GLY J:132 , MET J:133 , ILE J:135 , TYR J:136 , VAL J:209 , HIS J:212 , PHE J:216 , GLY J:220 , ASN J:222 , ANJ J:505
BINDING SITE FOR RESIDUE HEM J 501
10
CC8
SOFTWARE
GLN J:58 , GLY J:62 , ILE J:63 , ARG J:94 , HIS J:97 , THR J:142 , GLY J:146 , LEU J:149 , PRO J:150 , HIS J:198 , TYR J:199 , PRO J:202
BINDING SITE FOR RESIDUE HEM J 502
11
CC9
SOFTWARE
VAL K:35 , CYS K:36 , CYS K:39 , HIS K:40 , LEU K:94 , ASN K:96 , MET K:103 , ARG K:107 , TYR K:130 , LEU K:135 , PHE K:160 , ILE K:183 , ALA K:184 , MET K:185 , PRO K:188
BINDING SITE FOR RESIDUE HEM K 301
12
DC1
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
13
EC3
SOFTWARE
PHE G:144 , MET G:145 , GLY G:158 , VAL G:161 , ILE G:162 , VAL G:293 , PRO G:294 , GLU G:295 , PHE G:298 , TYR G:302 , MET G:336 , PHE G:337 , HIS L:152
BINDING SITE FOR RESIDUE SMA G 503
14
EC4
SOFTWARE
CYS I:151 , HIS I:152 , MET J:140 , MET J:145 , GLY J:158 , VAL J:161 , ILE J:162 , LEU J:180 , PHE J:194 , VAL J:293 , PRO J:294 , GLU J:295 , PHE J:298 , TYR J:302 , MET J:336 , ILE J:340
BINDING SITE FOR RESIDUE SMA J 503
15
EC9
SOFTWARE
MET G:44 , TRP G:47 , LEU G:103 , PHE G:113 , TYR G:117 , TYR G:118 , PHE G:263 , TRP G:296 , ARG G:358 , PHE G:367
BINDING SITE FOR RESIDUE LOP G 504
16
FC1
SOFTWARE
ASN J:42 , PHE J:113 , ARG J:114 , TYR J:117 , TYR J:118 , VAL J:262 , ARG J:358 , PHE J:374
BINDING SITE FOR RESIDUE LOP J 504
17
FC6
SOFTWARE
TRP G:45 , VAL G:49 , ALA G:52 , 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
18
FC7
SOFTWARE
ALA J:29 , TRP J:45 , VAL J:49 , ALA J:52 , ILE J:213 , PHE J:216 , PHE J:244 , 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:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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:
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_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
-
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(5, 30)
Info
all CATH domains
1a: CATH_2qjkB01 (B:1-221)
1b: CATH_2qjkE01 (E:1-221)
1c: CATH_2qjkH01 (H:1-221)
1d: CATH_2qjkK01 (K:1-221)
1e: CATH_2qjkN01 (N:1-221)
1f: CATH_2qjkQ01 (Q:1-221)
2a: CATH_2qjkA00 (A:3-430)
2b: CATH_2qjkM00 (M:3-430)
2c: CATH_2qjkP00 (P:3-430)
2d: CATH_2qjkD00 (D:3-430)
2e: CATH_2qjkG00 (G:3-430)
2f: CATH_2qjkJ00 (J:3-430)
3a: CATH_2qjkB02 (B:222-256)
3b: CATH_2qjkE02 (E:222-256)
3c: CATH_2qjkH02 (H:222-256)
3d: CATH_2qjkK02 (K:222-256)
3e: CATH_2qjkN02 (N:222-256)
3f: CATH_2qjkQ02 (Q:222-256)
4a: CATH_2qjkC01 (C:9-41)
4b: CATH_2qjkF01 (F:9-41)
4c: CATH_2qjkI01 (I:9-41)
4d: CATH_2qjkL01 (L:9-41)
4e: CATH_2qjkO01 (O:9-41)
4f: CATH_2qjkR01 (R:9-41)
5a: CATH_2qjkC02 (C:42-187)
5b: CATH_2qjkF02 (F:42-187)
5c: CATH_2qjkI02 (I:42-187)
5d: CATH_2qjkL02 (L:42-187)
5e: CATH_2qjkO02 (O:42-187)
5f: CATH_2qjkR02 (R: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
2qjkB01
B:1-221
1b
2qjkE01
E:1-221
1c
2qjkH01
H:1-221
1d
2qjkK01
K:1-221
1e
2qjkN01
N:1-221
1f
2qjkQ01
Q: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
2qjkA00
A:3-430
2b
2qjkM00
M:3-430
2c
2qjkP00
P:3-430
2d
2qjkD00
D:3-430
2e
2qjkG00
G:3-430
2f
2qjkJ00
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
2qjkB02
B:222-256
3b
2qjkE02
E:222-256
3c
2qjkH02
H:222-256
3d
2qjkK02
K:222-256
3e
2qjkN02
N:222-256
3f
2qjkQ02
Q:222-256
Homologous Superfamily
:
Single helix bin
(16)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
4a
2qjkC01
C:9-41
4b
2qjkF01
F:9-41
4c
2qjkI01
I:9-41
4d
2qjkL01
L:9-41
4e
2qjkO01
O:9-41
4f
2qjkR01
R: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
2qjkC02
C:42-187
5b
2qjkF02
F:42-187
5c
2qjkI02
I:42-187
5d
2qjkL02
L:42-187
5e
2qjkO02
O:42-187
5f
2qjkR02
R:42-187
[
close CATH info
]
Pfam Domains
(5, 30)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_2qjkP01 (P:102-277)
1b: PFAM_Cytochrom_B_N_2_2qjkP02 (P:102-277)
1c: PFAM_Cytochrom_B_N_2_2qjkP03 (P:102-277)
1d: PFAM_Cytochrom_B_N_2_2qjkP04 (P:102-277)
1e: PFAM_Cytochrom_B_N_2_2qjkP05 (P:102-277)
1f: PFAM_Cytochrom_B_N_2_2qjkP06 (P:102-277)
2a: PFAM_Cytochrom_C1_2qjkQ01 (Q:11-255)
2b: PFAM_Cytochrom_C1_2qjkQ02 (Q:11-255)
2c: PFAM_Cytochrom_C1_2qjkQ03 (Q:11-255)
2d: PFAM_Cytochrom_C1_2qjkQ04 (Q:11-255)
2e: PFAM_Cytochrom_C1_2qjkQ05 (Q:11-255)
2f: PFAM_Cytochrom_C1_2qjkQ06 (Q:11-255)
3a: PFAM_Rieske_2qjkR01 (R:95-180)
3b: PFAM_Rieske_2qjkR02 (R:95-180)
3c: PFAM_Rieske_2qjkR03 (R:95-180)
3d: PFAM_Rieske_2qjkR04 (R:95-180)
3e: PFAM_Rieske_2qjkR05 (R:95-180)
3f: PFAM_Rieske_2qjkR06 (R:95-180)
4a: PFAM_UCR_Fe_S_N_2qjkR07 (R:9-41)
4b: PFAM_UCR_Fe_S_N_2qjkR08 (R:9-41)
4c: PFAM_UCR_Fe_S_N_2qjkR09 (R:9-41)
4d: PFAM_UCR_Fe_S_N_2qjkR10 (R:9-41)
4e: PFAM_UCR_Fe_S_N_2qjkR11 (R:9-41)
4f: PFAM_UCR_Fe_S_N_2qjkR12 (R:9-41)
5a: PFAM_Cytochrom_B_C_2qjkP07 (P:282-416)
5b: PFAM_Cytochrom_B_C_2qjkP08 (P:282-416)
5c: PFAM_Cytochrom_B_C_2qjkP09 (P:282-416)
5d: PFAM_Cytochrom_B_C_2qjkP10 (P:282-416)
5e: PFAM_Cytochrom_B_C_2qjkP11 (P:282-416)
5f: PFAM_Cytochrom_B_C_2qjkP12 (P:282-416)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
1a
Cytochrom_B_N_2-2qjkP01
P:102-277
1b
Cytochrom_B_N_2-2qjkP02
P:102-277
1c
Cytochrom_B_N_2-2qjkP03
P:102-277
1d
Cytochrom_B_N_2-2qjkP04
P:102-277
1e
Cytochrom_B_N_2-2qjkP05
P:102-277
1f
Cytochrom_B_N_2-2qjkP06
P:102-277
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
2a
Cytochrom_C1-2qjkQ01
Q:11-255
2b
Cytochrom_C1-2qjkQ02
Q:11-255
2c
Cytochrom_C1-2qjkQ03
Q:11-255
2d
Cytochrom_C1-2qjkQ04
Q:11-255
2e
Cytochrom_C1-2qjkQ05
Q:11-255
2f
Cytochrom_C1-2qjkQ06
Q:11-255
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(8)
3a
Rieske-2qjkR01
R:95-180
3b
Rieske-2qjkR02
R:95-180
3c
Rieske-2qjkR03
R:95-180
3d
Rieske-2qjkR04
R:95-180
3e
Rieske-2qjkR05
R:95-180
3f
Rieske-2qjkR06
R:95-180
Clan
:
TAT
(4)
Family
:
UCR_Fe-S_N
(4)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
4a
UCR_Fe-S_N-2qjkR07
R:9-41
4b
UCR_Fe-S_N-2qjkR08
R:9-41
4c
UCR_Fe-S_N-2qjkR09
R:9-41
4d
UCR_Fe-S_N-2qjkR10
R:9-41
4e
UCR_Fe-S_N-2qjkR11
R:9-41
4f
UCR_Fe-S_N-2qjkR12
R: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-2qjkP07
P:282-416
5b
Cytochrom_B_C-2qjkP08
P:282-416
5c
Cytochrom_B_C-2qjkP09
P:282-416
5d
Cytochrom_B_C-2qjkP10
P:282-416
5e
Cytochrom_B_C-2qjkP11
P:282-416
5f
Cytochrom_B_C-2qjkP12
P:282-416
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