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.
3S8G
Asym. Unit
Info
Asym.Unit (272 KB)
Biol.Unit 1 (255 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.8 A STRUCTURE OF BA3 CYTOCHROME C OXIDASE MUTANT (A120F) FROM THERMUS THERMOPHILUS IN LIPID ENVIRONMENT
Authors
:
T. Tiefenbrunn, W. Liu, Y. Chen, V. Katritch, C. D. Stout, J. A. Fee, V. Ch
Date
:
27 May 11 (Deposition) - 03 Aug 11 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Complex Iv, Electron Transport, Proton Pump, Oxidoreductase, Respiratory Chain, Membrane Protein, Lipid Cubic Phase, Monoolein, Peroxide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Tiefenbrunn, W. Liu, Y. Chen, V. Katritch, C. D. Stout, J. A. Fee, V. Cherezov
High Resolution Structure Of The Ba3 Cytochrome C Oxidase From Thermus Thermophilus In A Lipidic Environment.
Plos One V. 6 22348 2011
[
close entry info
]
Hetero Components
(6, 25)
Info
All Hetero Components
2a: DINUCLEAR COPPER ION (CUAa)
1a: COPPER (II) ION (CUa)
3a: HEME-AS (HASa)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5a: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCa)
5b: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCb)
5c: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCc)
5d: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCd)
5e: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCe)
5f: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCf)
5g: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCg)
5h: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCh)
5i: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCi)
5j: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCj)
5k: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCk)
5l: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCl)
5m: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCm)
5n: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCn)
5o: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCo)
5p: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCp)
5q: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCq)
5r: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCr)
5s: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCs)
5t: (2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTA... (OLCt)
6a: PEROXIDE ION (PERa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
1
Ligand/Ion
COPPER (II) ION
2
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
3
HAS
1
Ligand/Ion
HEME-AS
4
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
OLC
20
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6
PER
1
Ligand/Ion
PEROXIDE ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:39 , PRO A:40 , GLN A:42 , ALA A:43 , TYR A:46 , TYR A:65 , LEU A:69 , HIS A:72 , ASN A:76 , ALA A:77 , LEU A:132 , TYR A:133 , PHE A:385 , HIS A:386 , ALA A:390 , THR A:394 , MET A:432 , MET A:435 , ARG A:449 , ARG A:450 , ALA A:451 , LEU A:477 , HOH A:579 , HOH A:586 , HOH A:587
BINDING SITE FOR RESIDUE HEM A 800
02
AC2
SOFTWARE
TYR A:133 , TRP A:229 , VAL A:236 , TYR A:237 , HIS A:282 , HIS A:283 , SER A:309 , LEU A:310 , ALA A:313 , LEU A:353 , PHE A:356 , GLY A:360 , GLY A:363 , ASN A:366 , ALA A:367 , ASP A:372 , HIS A:376 , HIS A:384 , PHE A:385 , GLN A:388 , ARG A:449 , PER A:563 , HOH A:589 , HOH A:609 , HOH A:610 , HOH A:613
BINDING SITE FOR RESIDUE HAS A 801
03
AC3
SOFTWARE
HIS A:233 , HIS A:282 , HIS A:283 , PER A:563
BINDING SITE FOR RESIDUE CU A 803
04
AC4
SOFTWARE
HIS A:233 , VAL A:236 , HIS A:283 , HOH A:618 , HAS A:801 , CU A:803
BINDING SITE FOR RESIDUE PER A 563
05
AC5
SOFTWARE
PRO A:358 , MET A:433 , HIS A:440 , OLC A:565 , OLC B:170 , PHE C:22 , ALA C:32
BINDING SITE FOR RESIDUE OLC A 564
06
AC6
SOFTWARE
OLC A:564 , OLC A:578
BINDING SITE FOR RESIDUE OLC A 565
07
AC7
SOFTWARE
TYR A:161 , OLC A:574 , OLC A:575
BINDING SITE FOR RESIDUE OLC A 566
08
AC8
SOFTWARE
PHE A:213 , LEU A:215 , TRP A:341 , TRP A:426 , OLC A:569 , OLC A:573
BINDING SITE FOR RESIDUE OLC A 567
09
AC9
SOFTWARE
PHE A:304 , ASP A:517 , LYS B:16 , LEU B:37 , ALA B:38 , OLC B:172
BINDING SITE FOR RESIDUE OLC A 568
10
BC1
SOFTWARE
SER A:212 , PHE A:213 , GLY A:214 , OLC A:567 , OLC A:577 , HOH A:1041
BINDING SITE FOR RESIDUE OLC A 569
11
BC2
SOFTWARE
TRP A:111 , OLC A:573 , OLC A:576
BINDING SITE FOR RESIDUE OLC A 570
12
BC3
SOFTWARE
TYR A:161 , LEU A:164 , ASP A:165 , ARG A:168 , OLC A:572
BINDING SITE FOR RESIDUE OLC A 571
13
BC4
SOFTWARE
TRP A:167 , ARG A:168 , GLY A:528 , OLC A:571 , HOH A:1157
BINDING SITE FOR RESIDUE OLC A 572
14
BC5
SOFTWARE
GLY A:104 , LEU A:108 , ALA A:464 , VAL A:468 , OLC A:567 , OLC A:570 , OLC A:574
BINDING SITE FOR RESIDUE OLC A 573
15
BC6
SOFTWARE
ASN A:102 , GLY A:104 , LEU A:105 , MET A:112 , LEU A:472 , OLC A:566 , OLC A:573 , OLC A:575
BINDING SITE FOR RESIDUE OLC A 574
16
BC7
SOFTWARE
ALA A:416 , OLC A:566 , OLC A:574 , HOH A:1023 , HOH A:1245
BINDING SITE FOR RESIDUE OLC A 575
17
BC8
SOFTWARE
LYS A:19 , TYR A:23 , TRP A:107 , TRP A:111 , OLC A:570
BINDING SITE FOR RESIDUE OLC A 576
18
BC9
SOFTWARE
ARG A:337 , TRP A:341 , OLC A:569 , HOH A:1230
BINDING SITE FOR RESIDUE OLC A 577
19
CC1
SOFTWARE
TRP A:441 , OLC A:565 , HOH A:1024 , HOH A:1025 , OLC B:170
BINDING SITE FOR RESIDUE OLC A 578
20
CC2
SOFTWARE
HIS B:114 , CYS B:149 , GLN B:151 , CYS B:153 , HIS B:157 , MET B:160
BINDING SITE FOR RESIDUE CUA B 802
21
CC3
SOFTWARE
PHE B:21 , LEU B:32 , TYR B:35 , OLC B:171 , TYR C:27 , PHE C:31 , OLC C:35
BINDING SITE FOR RESIDUE OLC B 169
22
CC4
SOFTWARE
TRP A:441 , OLC A:564 , OLC A:578 , ARG B:141 , GLU B:144 , TYR B:145 , ARG C:33
BINDING SITE FOR RESIDUE OLC B 170
23
CC5
SOFTWARE
ALA B:13 , TYR B:14 , GLY B:17 , TRP B:18 , PHE B:21 , TYR B:35 , OLC B:169 , ILE C:12 , LEU C:17
BINDING SITE FOR RESIDUE OLC B 171
24
CC6
SOFTWARE
OLC A:568 , ALA B:42 , HOH B:1046
BINDING SITE FOR RESIDUE OLC B 172
25
CC7
SOFTWARE
OLC B:169 , ALA C:28 , HOH C:1027
BINDING SITE FOR RESIDUE OLC C 35
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: COX2_CUA (B:66-168)
2: COX2 (B:112-160)
3: COX1_CUB (A:229-283)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_THET8
66-168
1
B:66-168
2
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_THET8
112-160
1
B:112-160
3
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_THET8
229-283
1
A:229-283
[
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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3s8gb2 (B:41-168)
2a: SCOP_d3s8ga_ (A:)
3a: SCOP_d3s8gc_ (C:)
4a: SCOP_d3s8gb1 (B:3-40)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Periplasmic domain of cytochrome c oxidase subunit II
(70)
Protein domain
:
Cytochrome c oxidase
(62)
Thermus thermophilus, ba3 type [TaxId: 274]
(28)
1a
d3s8gb2
B:41-168
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Cytochrome c oxidase subunit I-like
(65)
Superfamily
:
Cytochrome c oxidase subunit I-like
(65)
Family
:
Cytochrome c oxidase subunit I-like
(65)
Protein domain
:
Bacterial ba3 type cytochrome c oxidase subunit I
(24)
Thermus thermophilus [TaxId: 274]
(24)
2a
d3s8ga_
A:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Family
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Protein domain
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Thermus thermophilus [TaxId: 274]
(23)
3a
d3s8gc_
C:
Fold
:
Transmembrane helix hairpin
(84)
Superfamily
:
Cytochrome c oxidase subunit II-like, transmembrane region
(66)
Family
:
Cytochrome c oxidase subunit II-like, transmembrane region
(57)
Protein domain
:
Bacterial ba3 type cytochrome c oxidase subunit II
(18)
Thermus thermophilus [TaxId: 274]
(18)
4a
d3s8gb1
B:3-40
[
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
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 (272 KB)
Header - Asym.Unit
Biol.Unit 1 (255 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
3S8G
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help