PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4U3F
Asym. Unit
Info
Asym.Unit (683 KB)
Biol.Unit 1 (666 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CYTOCHROME BC1 COMPLEX FROM CHICKEN WITH DESIGNED INHIBITOR BOUND
Authors
:
L. -S. Huang, X. -L. Zhu, G. F. Yang, E. A. Berry
Date
:
21 Jul 14 (Deposition) - 29 Jul 15 (Release) - 26 Oct 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.23
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,N,O,P,Q,R,S,T,U,V,W
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,N,O,P,Q,R,S,T,U,V,W (1x)
Keywords
:
Cytochrome Bc1, Membrane Protein, Heme Protein, Rieske Iron Sulfur Protein, Cytochrome B, Cytochrome C1, Ubiquinone, Complex Iii, Strobilurins, Azoxystrobin, Stigmatellin, Oxidoreductase, Redox Enzyme Respiratory Chain, Electron Transport, Heme, Inner Membrane, Membrane Binding, Mitochondrion, Transmembrane, Iron, Mitochondrial Inner Membrane, Respiratory Chain, 2Fe-2S, Iron-Sulfur, Metal- Binding, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. -F. Hao, S. -G. Yang, W. Huang, L. Wang, Y. -Q. Shen, W. -L. Tu, H. Li, L. -S. Huang, J. -W. Wu, E. A. Berry, G. -F. Yang
Rational Design Of Highly Potent And Slow-Binding Cytochrom Bc1 Inhibitor As Fungicide By Computational Substitution Optimization
Sci Rep V. 5 2015
[
close entry info
]
Hetero Components
(12, 63)
Info
All Hetero Components
01a: B-OCTYLGLUCOSIDE (BOGa)
01b: B-OCTYLGLUCOSIDE (BOGb)
01c: B-OCTYLGLUCOSIDE (BOGc)
02a: CARDIOLIPIN (CDLa)
02b: CARDIOLIPIN (CDLb)
02c: CARDIOLIPIN (CDLc)
02d: CARDIOLIPIN (CDLd)
03a: FE2/S2 (INORGANIC) CLUSTER (FESa)
03b: FE2/S2 (INORGANIC) CLUSTER (FESb)
04a: N-FORMYLMETHIONINE (FMEa)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
06a: HEME C (HECa)
06b: HEME C (HECb)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
07c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
07d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
08a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
09a: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEa)
09b: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEb)
09c: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEc)
09d: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEd)
09e: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEe)
09f: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEf)
09g: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEg)
09h: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEh)
09i: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEi)
09j: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEj)
09k: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEk)
09l: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEl)
09m: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEm)
09n: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEn)
10a: UBIQUINONE-10 (U10a)
10b: UBIQUINONE-10 (U10b)
11a: (UNKa)
11b: (UNKb)
11c: (UNKc)
11d: (UNKd)
11e: (UNKe)
11f: (UNKf)
11g: (UNKg)
11h: (UNKh)
11i: (UNKi)
11j: (UNKj)
11k: (UNKk)
11l: (UNKl)
11m: (UNKm)
11n: (UNKn)
11o: (UNKo)
11p: (UNKp)
11q: (UNKq)
11r: (UNKr)
11s: (UNKs)
11t: (UNKt)
11u: (UNKu)
11v: (UNKv)
11w: (UNKw)
11x: (UNKx)
11y: (UNKy)
11z: (UNKz)
12a: METHYL (2E)-3-METHOXY-2-(2-{[(5-ME... (Y52a)
12b: METHYL (2E)-3-METHOXY-2-(2-{[(5-ME... (Y52b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
3
Ligand/Ion
B-OCTYLGLUCOSIDE
2
CDL
4
Ligand/Ion
CARDIOLIPIN
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
5
GOL
2
Ligand/Ion
GLYCEROL
6
HEC
2
Ligand/Ion
HEME C
7
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
9
PEE
14
Ligand/Ion
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
10
U10
2
Ligand/Ion
UBIQUINONE-10
11
UNK
26
Mod. Amino Acid
12
Y52
2
Ligand/Ion
METHYL (2E)-3-METHOXY-2-(2-{[(5-METHOXY-1,3-BENZOTHIAZOL-2-YL)SULFANYL]METHYL}PHENYL)PROP-2-ENOATE
[
close Hetero Component info
]
Sites
(37, 37)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:442 , ILE C:230 , PEE C:510 , PEE E:502
binding site for residue PEE A 501
02
AC2
SOFTWARE
GLN C:45 , ILE C:46 , GLY C:49 , LEU C:50 , ALA C:53 , ARG C:81 , HIS C:84 , PHE C:91 , THR C:127 , GLY C:131 , LEU C:134 , PRO C:135 , HIS C:183 , PHE C:184 , PRO C:187
binding site for residue HEM C 501
03
AC3
SOFTWARE
TRP C:32 , GLY C:35 , LEU C:38 , PHE C:91 , HIS C:98 , ILE C:99 , ARG C:101 , SER C:107 , THR C:113 , TRP C:114 , GLY C:117 , THR C:194 , HIS C:197 , LEU C:198 , LEU C:201 , SER C:206 , ASN C:207 , U10 C:504
binding site for residue HEM C 502
04
AC4
SOFTWARE
MET C:125 , ALA C:126 , PHE C:129 , TYR C:132 , VAL C:133 , GLY C:143 , ALA C:144 , ILE C:147 , LYS C:270 , PRO C:271 , GLU C:272 , TYR C:274 , PHE C:275 , PEE C:509
binding site for residue Y52 C 503
05
AC5
SOFTWARE
SER C:18 , LEU C:19 , LEU C:22 , SER C:36 , ALA C:39 , LEU C:198 , HIS C:202 , SER C:206 , PHE C:221 , ASP C:229 , HEM C:502
binding site for residue U10 C 504
06
AC6
SOFTWARE
TRP C:31 , PHE C:96 , LEU C:97 , GLY C:100 , TYR C:104 , TYR C:105 , THR C:317 , GLN C:323 , PHE C:326 , TRP C:327 , LEU C:333 , THR C:337 , TYR C:359 , TYR F:29 , GLN G:44 , VAL G:48 , CDL G:101
binding site for residue PEE C 505
07
AC7
SOFTWARE
HIS C:346
binding site for residue MES C 506
08
AC8
SOFTWARE
HIS C:69 , ASP D:44 , TYR D:90
binding site for residue PEE C 507
09
AC9
SOFTWARE
PHE C:64 , ARG C:81 , ASN C:256 , PHE C:257 , TYR D:115
binding site for residue GOL C 508
10
AD1
SOFTWARE
THR C:123 , PHE C:129 , PHE C:151 , LEU C:182 , LEU C:185 , LEU C:186 , PHE C:188 , ALA C:189 , GLY C:192 , Y52 C:503
binding site for residue PEE C 509
11
AD2
SOFTWARE
PEE A:501 , ILE C:20 , HIS C:222
binding site for residue PEE C 510
12
AD3
SOFTWARE
VAL D:36 , CYS D:37 , CYS D:40 , HIS D:41 , ASN D:105 , PRO D:110 , ARG D:120 , TYR D:126 , PHE D:153 , GLY D:159 , MET D:160 , PRO D:163 , ILE D:164
binding site for residue HEC D 501
13
AD4
SOFTWARE
ALA C:30 , LYS C:228 , LEU C:231 , GLY C:232 , LEU C:235 , LYS D:223 , ARG D:224 , ARG F:73 , ILE G:29 , ALA G:33 , CDL G:101
binding site for residue CDL D 502
14
AD5
SOFTWARE
TYR C:76 , GLN D:200 , ARG D:203 , MET D:204 , LYS D:207 , ILE D:211 , ASN E:53 , GLN E:57
binding site for residue BOG D 503
15
AD6
SOFTWARE
CYS E:139 , HIS E:141 , LEU E:142 , CYS E:158 , HIS E:161 , SER E:163
binding site for residue FES E 501
16
AD7
SOFTWARE
TYR A:442 , PEE A:501 , ILE C:230 , TYR E:37 , THR E:40 , CYS E:44 , THR E:47 , VAL E:54 , PEE E:503 , PHE J:14 , VAL J:25
binding site for residue PEE E 502
17
AD8
SOFTWARE
LEU C:233 , LEU C:237 , LEU C:241 , MET D:204 , VAL E:54 , GLN E:57 , PEE E:502
binding site for residue PEE E 503
18
AD9
SOFTWARE
SER C:29 , ALA C:30 , TRP C:31 , TYR C:105 , PEE C:505 , CDL D:502 , VAL G:37 , ARG G:40 , PHE G:41 , GLN G:44
binding site for residue CDL G 101
19
AE1
SOFTWARE
TYR N:442
binding site for residue PEE N 501
20
AE2
SOFTWARE
ILE P:20 , SER P:36 , VAL P:40 , PHE P:221 , HIS P:222 , SER P:226 , U10 P:405
binding site for residue PEE P 401
21
AE3
SOFTWARE
GLN P:45 , ILE P:46 , GLY P:49 , LEU P:50 , ALA P:53 , ARG P:81 , HIS P:84 , PHE P:91 , THR P:127 , GLY P:131 , LEU P:134 , PRO P:135 , HIS P:183 , PHE P:184 , PRO P:187
binding site for residue HEM P 402
22
AE4
SOFTWARE
TRP P:32 , GLY P:35 , LEU P:38 , PHE P:91 , HIS P:98 , ILE P:99 , ARG P:101 , SER P:107 , THR P:113 , TRP P:114 , GLY P:117 , THR P:194 , HIS P:197 , LEU P:198 , LEU P:201 , SER P:206 , ASN P:207
binding site for residue HEM P 403
23
AE5
SOFTWARE
LEU P:122 , MET P:125 , ALA P:126 , ALA P:128 , PHE P:129 , TYR P:132 , VAL P:133 , GLY P:143 , ALA P:144 , ILE P:147 , LYS P:270 , PRO P:271 , GLU P:272 , TYR P:274 , PHE P:275
binding site for residue Y52 P 404
24
AE6
SOFTWARE
SER P:18 , LEU P:22 , SER P:36 , LEU P:198 , LEU P:201 , HIS P:202 , SER P:206 , PHE P:221 , ASP P:229 , PEE P:401 , HOH P:502
binding site for residue U10 P 405
25
AE7
SOFTWARE
PEE R:502
binding site for residue BOG P 406
26
AE8
SOFTWARE
TRP P:31 , PHE P:96 , LEU P:97 , GLY P:100 , TYR P:104 , TYR P:105 , THR P:317 , GLN P:323 , PHE P:326 , TRP P:327 , LEU P:333 , LEU P:334 , TYR P:359 , TYR S:29 , CDL T:101
binding site for residue PEE P 407
27
AE9
SOFTWARE
PHE P:64 , ARG P:81 , ASN P:256 , PHE P:257 , TYR Q:115
binding site for residue GOL P 408
28
AF1
SOFTWARE
LEU P:122 , THR P:123 , PHE P:129 , PHE P:151 , ALA P:165 , PHE P:179 , LEU P:182 , LEU P:186
binding site for residue PEE P 409
29
AF2
SOFTWARE
PHE P:188
binding site for residue PEE P 410
30
AF3
SOFTWARE
SER P:61 , HIS P:69 , TYR Q:45 , TYR Q:90
binding site for residue PEE P 411
31
AF4
SOFTWARE
ALA P:30 , LYS P:228 , GLY P:232 , MET P:236 , TYR Q:220 , LYS Q:223 , ARG Q:224 , ALA T:33 , VAL T:37 , CDL T:101
binding site for residue CDL Q 502
32
AF5
SOFTWARE
TYR P:76 , GLN Q:200 , ARG Q:203 , MET Q:204 , LYS Q:207 , ASN R:53 , GLN R:57
binding site for residue BOG Q 503
33
AF6
SOFTWARE
CYS R:139 , HIS R:141 , LEU R:142 , CYS R:144 , CYS R:158 , HIS R:161 , SER R:163
binding site for residue FES R 501
34
AF7
SOFTWARE
TYR N:442 , BOG P:406 , MET Q:222 , TYR R:37 , THR R:40 , CYS R:44 , THR R:47 , VAL W:25 , GLU W:32
binding site for residue PEE R 502
35
AF8
SOFTWARE
SER P:29 , ALA P:30 , TRP P:31 , TYR P:105 , PEE P:407 , CDL Q:502 , ARG T:40 , PHE T:41 , GLN T:44
binding site for residue CDL T 101
36
AF9
SOFTWARE
VAL Q:36 , CYS Q:37 , SER Q:38 , ALA Q:39 , HIS Q:41 , PRO Q:94 , TYR Q:95 , ASN Q:105 , PRO Q:110 , ARG Q:120 , TYR Q:126 , PHE Q:153 , GLY Q:159 , MET Q:160 , PRO Q:163 , ILE Q:164
binding site for Di-peptide HEC Q 501 and CYS Q 40
37
AG1
SOFTWARE
VAL Q:32 , TYR Q:33 , VAL Q:36 , SER Q:38 , ALA Q:39 , CYS Q:40 , HIS Q:41 , ASN Q:105 , PRO Q:110 , ARG Q:120 , TYR Q:126 , PHE Q:153 , GLY Q:159 , MET Q:160 , PRO Q:163 , ILE Q:164
binding site for Di-peptide HEC Q 501 and CYS Q 37
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Asymmetric Unit 1
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)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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
]
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:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (683 KB)
Header - Asym.Unit
Biol.Unit 1 (666 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4U3F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help