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.
3BVD
Asym. Unit
Info
Asym.Unit (111 KB)
Biol.Unit 1 (106 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF SURFACE-ENGINEERED CYTOCHROME BA3 OXIDASE FROM THERMUS THERMOPHILUS UNDER XENON PRESSURE, 100PSI 5MIN
Authors
:
V. M. Luna, Y. Chen, J. A. Fee, C. D. Stout
Date
:
07 Jan 08 (Deposition) - 20 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.37
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Cytochrome Ba3 Oxidase, Heme, Integral Membrane Protein, Copper, Electron Transport, Hydrogen Ion Transport, Ion Transport, Iron, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport, Formylation, Xenon
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Luna, Y. Chen, J. A. Fee, C. D. Stout
Crystallographic Studies Of Xe And Kr Binding Within The Large Internal Cavity Of Cytochrome Ba3 From Thermus Thermophilus: Structural Analysis And Role Of Oxygen Transport Channels In The Heme-Cu Oxidases.
Biochemistry V. 47 4657 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 11)
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: XENON (XEa)
5b: XENON (XEb)
5c: XENON (XEc)
5d: XENON (XEd)
5e: XENON (XEe)
5f: XENON (XEf)
5g: XENON (XEg)
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
XE
7
Ligand/Ion
XENON
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:233 , HIS A:282 , HIS A:283
BINDING SITE FOR RESIDUE CU A 803
2
AC2
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 , TYR A:133 , PHE A:385 , HIS A:386 , VAL A:389 , ALA A:390 , THR A:394 , MET A:432 , ARG A:449 , ARG A:450 , ALA A:451
BINDING SITE FOR RESIDUE HEM A 800
3
AC3
SOFTWARE
TYR A:133 , TRP A:229 , VAL A:236 , TYR A:237 , TRP A:239 , HIS A:282 , THR A:302 , SER A:309 , ALA A:313 , ALA A:317 , LEU A:353 , LEU A:354 , PHE A:356 , GLY A:360 , GLY A:363 , ASN A:366 , ALA A:367 , ASP A:372 , HIS A:376 , VAL A:381 , HIS A:384 , PHE A:385 , GLN A:388 , ARG A:449
BINDING SITE FOR RESIDUE HAS A 801
4
AC4
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
5
AC5
SOFTWARE
TYR A:133 , GLY A:232
BINDING SITE FOR RESIDUE XE A 805
6
AC6
SOFTWARE
LEU A:208
BINDING SITE FOR RESIDUE XE A 807
7
AC7
SOFTWARE
VAL A:201
BINDING SITE FOR RESIDUE XE A 808
8
AC8
SOFTWARE
PHE A:228 , XE A:810
BINDING SITE FOR RESIDUE XE A 809
9
AC9
SOFTWARE
PHE A:228 , GLY A:232 , XE A:809
BINDING SITE FOR RESIDUE XE A 810
[
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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3bvdb1 (B:37-168)
2a: SCOP_d3bvdc1 (C:2-34)
3a: SCOP_d3bvdb2 (B:3-36)
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
d3bvdb1
B:37-168
Class
:
Membrane and cell surface proteins and peptides
(2046)
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)
2a
d3bvdc1
C:2-34
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)
3a
d3bvdb2
B:3-36
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_3bvdA00 (A:13-562)
2a: CATH_3bvdB01 (B:3-46)
3a: CATH_3bvdB02 (B:47-168)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Thermus thermophilus. Strain: hb8.
(1)
1a
3bvdA00
A:13-562
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Thermus thermophilus. Strain: hb8.
(1)
2a
3bvdB01
B:3-46
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Thermus thermophilus. Strain: hb8.
(1)
3a
3bvdB02
B:47-168
[
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 (111 KB)
Header - Asym.Unit
Biol.Unit 1 (106 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
3BVD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help