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1SQQ
Biol. Unit 1
Info
Asym.Unit (355 KB)
Biol.Unit 1 (674 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF BOVINE BC1 WITH METHOXY ACRYLATE STILBENE (MOAS)
Authors
:
L. Esser, B. Quinn, Y. F. Li, M. Zhang, M. Elberry, L. Yu, C. A. Yu, D. Xia
Date
:
19 Mar 04 (Deposition) - 25 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K (2x)
Keywords
:
Cytochrome Bc1, Qo Inhibitor, Membrane Protein, Electron Transport, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Esser, B. Quinn, Y. F. Li, M. Zhang, M. Elberry, L. Yu, C. A. Yu, D. Xia
Crystallographic Studies Of Quinol Oxidation Site Inhibitors: A Modified Classification Of Inhibitors For The Cytochrome Bc(1) Complex.
J. Mol. Biol. V. 341 281 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3a: METHYL (2Z)-3-METHOXY-2-{2-[(E)-2-... (OSTa)
4a: UBIQUINONE-2 (UQ2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
OST
2
Ligand/Ion
METHYL (2Z)-3-METHOXY-2-{2-[(E)-2-PHENYLVINYL]PHENYL}ACRYLATE
4
UQ2
2
Ligand/Ion
UBIQUINONE-2
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN C:44 , GLY C:48 , LEU C:51 , ARG C:80 , HIS C:83 , ALA C:87 , PHE C:90 , THR C:126 , ALA C:127 , GLY C:130 , LEU C:133 , PRO C:134 , PHE C:179 , HIS C:182 , PHE C:183 , PRO C:186
BINDING SITE FOR RESIDUE HEM C 381
2
AC2
SOFTWARE
TRP C:31 , GLY C:34 , LEU C:37 , HIS C:97 , VAL C:98 , ARG C:100 , SER C:106 , TRP C:113 , GLY C:116 , VAL C:117 , LEU C:119 , HIS C:196 , LEU C:200 , SER C:205 , ASN C:206 , UQ2 C:383 , HOH C:1001
BINDING SITE FOR RESIDUE HEM C 382
3
AC3
SOFTWARE
PHE C:18 , ILE C:27 , SER C:35 , ALA C:193 , LEU C:197 , HIS C:201 , SER C:205 , PHE C:220 , ASP C:228 , HEM C:382 , HOH C:1006 , HOH C:1007
BINDING SITE FOR RESIDUE UQ2 C 383
4
AC4
SOFTWARE
PHE C:128 , TYR C:131 , VAL C:132 , GLY C:142 , ALA C:143 , ILE C:146 , ILE C:268 , LYS C:269 , PRO C:270 , GLU C:271 , TYR C:273 , PHE C:274 , LEU C:294
BINDING SITE FOR RESIDUE OST C 384
5
AC5
SOFTWARE
CYS D:37 , CYS D:40 , HIS D:41 , ASN D:105 , LEU D:109 , PRO D:110 , PRO D:111 , ARG D:120 , TYR D:126 , GLY D:159 , MET D:160 , PRO D:163 , ILE D:164
BINDING SITE FOR RESIDUE HEM D 242
6
AC6
SOFTWARE
CYS E:139 , HIS E:141 , LEU E:142 , CYS E:144 , CYS E:158 , HIS E:161 , GLY E:162 , SER E:163
BINDING SITE FOR RESIDUE FES E 197
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_QCR2_BOVIN_001 (T27R, chain B, )
2: VAR_CYB_BOVIN_001 (F90V, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_QCR2_BOVIN_001
*
T
41
R
QCR2_BOVIN
---
---
B
T
27
R
2
UniProt
VAR_CYB_BOVIN_001
*
F
90
V
CYB_BOVIN
---
---
C
F
90
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: INSULINASE (B:54-77)
2: CYTC (D:24-125)
3: RIESKE (E:109-194)
4: CYTB_CTER (C:210-379)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INSULINASE
PS00143
Insulinase family, zinc-binding region signature.
QCR2_BOVIN
68-91
2
B:54-77
2
CYTC
PS51007
Cytochrome c family profile.
CY1_BOVIN
108-209
2
D:24-125
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_BOVIN
187-272
2
E:109-194
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_BOVIN
210-379
2
C:210-379
[
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
(14, 16)
Info
All SCOP Domains
01a: SCOP_d1sqqd1 (D:1-195)
02a: SCOP_d1sqqe2 (E:70-196)
03a: SCOP_d1sqqb2 (B:236-439)
04a: SCOP_d1sqqa1 (A:1-233)
04b: SCOP_d1sqqa2 (A:234-446)
04c: SCOP_d1sqqb1 (B:17-235)
05a: SCOP_d1sqqi_ (I:)
06a: SCOP_d1sqqf1 (F:6-110)
07a: SCOP_d1sqqc1 (C:261-379)
08a: SCOP_d1sqqc2 (C:2-260)
09a: SCOP_d1sqqh_ (H:)
10a: SCOP_d1sqqd2 (D:196-241)
11a: SCOP_d1sqqe1 (E:1-69)
12a: SCOP_d1sqqj_ (J:)
13a: SCOP_d1sqqk1 (K:1-54)
14a: SCOP_d1sqqg_ (G:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
Cytochrome bc1 domain
(36)
Protein domain
:
automated matches
(9)
Cow (Bos taurus) [TaxId: 9913]
(1)
01a
d1sqqd1
D:1-195
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
automated matches
(8)
Cow (Bos taurus) [TaxId: 9913]
(1)
02a
d1sqqe2
E:70-196
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LuxS/MPP-like metallohydrolase
(89)
Superfamily
:
LuxS/MPP-like metallohydrolase
(89)
Family
:
automated matches
(9)
Protein domain
:
automated matches
(9)
Cow (Bos taurus) [TaxId: 9913]
(1)
03a
d1sqqb2
B:236-439
Family
:
MPP-like
(65)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
04a
d1sqqa1
A:1-233
04b
d1sqqa2
A:234-446
04c
d1sqqb1
B:17-235
Fold
:
Non-globular alpha+beta subunits of globular proteins
(21)
Superfamily
:
Non-globular alpha+beta subunits of globular proteins
(21)
Family
:
Ubiquinol-cytochrome c reductase 8 kDa protein
(17)
Protein domain
:
automated matches
(3)
Cow (Bos taurus) [TaxId: 9913]
(3)
05a
d1sqqi_
I:
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(21)
Cow (Bos taurus) [TaxId: 9913]
(14)
06a
d1sqqf1
F:6-110
Fold
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Superfamily
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Cow (Bos taurus) [TaxId: 9913]
(1)
07a
d1sqqc1
C:261-379
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Transmembrane di-heme cytochromes
(48)
Family
:
Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Protein domain
:
automated matches
(11)
Cow (Bos taurus) [TaxId: 9913]
(1)
08a
d1sqqc2
C:2-260
Fold
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
automated matches
(16)
Cow (Bos taurus) [TaxId: 9913]
(6)
09a
d1sqqh_
H:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(36)
Family
:
automated matches
(9)
Protein domain
:
automated matches
(9)
Cow (Bos taurus) [TaxId: 9913]
(1)
10a
d1sqqd2
D:196-241
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Cow (Bos taurus) [TaxId: 9913]
(1)
11a
d1sqqe1
E:1-69
Superfamily
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(25)
Cow (Bos taurus) [TaxId: 9913]
(18)
12a
d1sqqj_
J:
Superfamily
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(15)
Family
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(15)
Protein domain
:
Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(12)
Cow (Bos taurus) [TaxId: 9913]
(12)
13a
d1sqqk1
K:1-54
Superfamily
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(28)
Cow (Bos taurus) [TaxId: 9913]
(18)
14a
d1sqqg_
G:
[
close SCOP info
]
CATH Domains
(12, 15)
Info
all CATH domains
01a: CATH_1sqqA02 (A:239-442)
01b: CATH_1sqqB01 (B:17-227)
01c: CATH_1sqqB02 (B:239-439)
01d: CATH_1sqqA01 (A:14-228)
02a: CATH_1sqqD01 (D:1-196)
03a: CATH_1sqqF00 (F:6-110)
04a: CATH_1sqqH00 (H:9-78)
05a: CATH_1sqqC00 (C:2-379)
06a: CATH_1sqqD02 (D:197-241)
07a: CATH_1sqqG00 (G:1-75)
08a: CATH_1sqqK00 (K:1-54)
09a: CATH_1sqqJ00 (J:3-61)
10a: CATH_1sqqE01 (E:1-64)
11a: CATH_1sqqE02 (E:65-196)
12a: CATH_1sqqI00 (I:1-57)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Cattle (Bos taurus)
(17)
01a
1sqqA02
A:239-442
01b
1sqqB01
B:17-227
01c
1sqqB02
B:239-439
01d
1sqqA01
A:14-228
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Cattle (Bos taurus)
(18)
02a
1sqqD01
D:1-196
Topology
:
Cytochrome Bc1 Complex; Chain F
(39)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain F
(39)
Cattle (Bos taurus)
(17)
03a
1sqqF00
F:6-110
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.20, no name defined]
(39)
Cattle (Bos taurus)
(17)
04a
1sqqH00
H:9-78
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Cattle (Bos taurus)
(17)
05a
1sqqC00
C:2-379
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)
Cattle (Bos taurus)
(17)
06a
1sqqD02
D:197-241
Homologous Superfamily
:
[code=1.20.5.210, no name defined]
(39)
Cattle (Bos taurus)
(17)
07a
1sqqG00
G:1-75
Homologous Superfamily
:
[code=1.20.5.220, no name defined]
(20)
Cattle (Bos taurus)
(14)
08a
1sqqK00
K:1-54
Homologous Superfamily
:
[code=1.20.5.260, no name defined]
(39)
Cattle (Bos taurus)
(17)
09a
1sqqJ00
J:3-61
Homologous Superfamily
:
[code=1.20.5.270, no name defined]
(39)
Cattle (Bos taurus)
(17)
10a
1sqqE01
E:1-64
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Cattle (Bos taurus)
(18)
11a
1sqqE02
E:65-196
Architecture
:
Ribbon
(789)
Topology
:
Cytochrome Bc1 Complex; Chain I
(29)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain I
(29)
Cattle (Bos taurus)
(17)
12a
1sqqI00
I:1-57
[
close CATH info
]
Pfam Domains
(13, 15)
Info
all PFAM domains
01a: PFAM_Cytochrom_B_N_2_1sqqC01 (C:88-253)
02a: PFAM_Cytochrom_C1_1sqqD01 (D:12-230)
03a: PFAM_Rieske_1sqqE01 (E:77-188)
04a: PFAM_Peptidase_M16_1sqqA01 (A:24-171)
04b: PFAM_Peptidase_M16_1sqqB01 (B:34-180)
05a: PFAM_Peptidase_M16_C_1sqqA02 (A:176-361)
05b: PFAM_Peptidase_M16_C_1sqqB02 (B:185-364)
06a: PFAM_UcrQ_1sqqG01 (G:1-75)
07a: PFAM_Cytochrom_B_C_1sqqC02 (C:258-359)
08a: PFAM_UCR_14kD_1sqqF01 (F:6-106)
09a: PFAM_UCR_6_4kD_1sqqK01 (K:1-54)
10a: PFAM_UCR_TM_1sqqE02 (E:1-67)
11a: PFAM_UCR_UQCRX_QCR9_1sqqJ01 (J:6-60)
12a: PFAM_UCR_hinge_1sqqH01 (H:14-78)
13a: PFAM_Ubiq_Cytc_red_N_1sqqI01 (I:1-57)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Bos taurus (Bovine)
(13)
01a
Cytochrom_B_N_2-1sqqC01
C:88-253
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Bos taurus (Bovine)
(13)
02a
Cytochrom_C1-1sqqD01
D:12-230
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Bos taurus (Bovine)
(13)
03a
Rieske-1sqqE01
E:77-188
Clan
:
Peptidase_ME
(35)
Family
:
Peptidase_M16
(29)
Bos taurus (Bovine)
(13)
04a
Peptidase_M16-1sqqA01
A:24-171
04b
Peptidase_M16-1sqqB01
B:34-180
Family
:
Peptidase_M16_C
(29)
Bos taurus (Bovine)
(13)
05a
Peptidase_M16_C-1sqqA02
A:176-361
05b
Peptidase_M16_C-1sqqB02
B:185-364
Clan
:
UcrQ-like
(20)
Family
:
UcrQ
(20)
Bos taurus (Bovine)
(13)
06a
UcrQ-1sqqG01
G:1-75
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Bos taurus (Bovine)
(13)
07a
Cytochrom_B_C-1sqqC02
C:258-359
Clan
:
no clan defined [family: UCR_14kD]
(20)
Family
:
UCR_14kD
(20)
Bos taurus (Bovine)
(13)
08a
UCR_14kD-1sqqF01
F:6-106
Clan
:
no clan defined [family: UCR_6-4kD]
(11)
Family
:
UCR_6-4kD
(11)
Bos taurus (Bovine)
(11)
09a
UCR_6-4kD-1sqqK01
K:1-54
Clan
:
no clan defined [family: UCR_TM]
(20)
Family
:
UCR_TM
(20)
Bos taurus (Bovine)
(13)
10a
UCR_TM-1sqqE02
E:1-67
Clan
:
no clan defined [family: UCR_UQCRX_QCR9]
(20)
Family
:
UCR_UQCRX_QCR9
(20)
Bos taurus (Bovine)
(13)
11a
UCR_UQCRX_QCR9-1sqqJ01
J:6-60
Clan
:
no clan defined [family: UCR_hinge]
(20)
Family
:
UCR_hinge
(20)
Bos taurus (Bovine)
(13)
12a
UCR_hinge-1sqqH01
H:14-78
Clan
:
no clan defined [family: Ubiq-Cytc-red_N]
(17)
Family
:
Ubiq-Cytc-red_N
(17)
Bos taurus (Bovine)
(13)
13a
Ubiq-Cytc-red_N-1sqqI01
I:1-57
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Asymmetric Unit 1
Asymmetric Unit 2
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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Miscellaneous
Script
Example Commands
Example Command
Action
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)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (355 KB)
Header - Asym.Unit
Biol.Unit 1 (674 KB)
Header - Biol.Unit 1
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