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.
3EHB
Asym. Unit
Info
Asym.Unit (198 KB)
Biol.Unit 1 (186 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A D-PATHWAY MUTATION DECOUPLES THE PARACOCCUS DENITRIFICANS CYTOCHROME C OXIDASE BY ALTERING THE SIDE CHAIN ORIENTATION OF A DISTANT, CONSERVED GLUTAMATE
Authors
:
J. Koepke, H. Mueller, G. Peng
Date
:
12 Sep 08 (Deposition) - 30 Sep 08 (Release) - 09 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.32
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Proton Pumping, Water Chain, Electron Transfer, Cell Inner Membrane, Cell Membrane, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport, Pyrrolidone Carboxylic Acid, Oxidoreductase/Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Durr, J. Koepke, P. Hellwig, H. Muller, H. Angerer, G. Peng, E. Olkhova, O. -M. H. Richter, B. Ludwig, H. Michel
A D-Pathway Mutation Decouples The Paracoccusdenitrificans Cytochrome C Oxidase By Altering The Side-Chain Orientation Of A Distant Conserved Glutamate
J. Mol. Biol. V. 384 865 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 29)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
3a: HEME-A (HEAa)
3b: HEME-A (HEAb)
4a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
4b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
4c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
4d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
4e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
4f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
4g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
4h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
4i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
5a: DODECYL-BETA-D-MALTOSIDE (LMTa)
5b: DODECYL-BETA-D-MALTOSIDE (LMTb)
5c: DODECYL-BETA-D-MALTOSIDE (LMTc)
5d: DODECYL-BETA-D-MALTOSIDE (LMTd)
5e: DODECYL-BETA-D-MALTOSIDE (LMTe)
5f: DODECYL-BETA-D-MALTOSIDE (LMTf)
5g: DODECYL-BETA-D-MALTOSIDE (LMTg)
5h: DODECYL-BETA-D-MALTOSIDE (LMTh)
5i: DODECYL-BETA-D-MALTOSIDE (LMTi)
5j: DODECYL-BETA-D-MALTOSIDE (LMTj)
5k: DODECYL-BETA-D-MALTOSIDE (LMTk)
5l: DODECYL-BETA-D-MALTOSIDE (LMTl)
6a: MAGNESIUM ION (MGa)
7a: PEROXIDE ION (PERa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
CU
3
Ligand/Ion
COPPER (II) ION
3
HEA
2
Ligand/Ion
HEME-A
4
LDA
9
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
5
LMT
12
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
6
MG
1
Ligand/Ion
MAGNESIUM ION
7
PER
1
Ligand/Ion
PEROXIDE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:36 , GLY A:40 , VAL A:47 , THR A:50 , MET A:53 , ARG A:54 , TRP A:87 , ILE A:91 , HIS A:94 , MET A:98 , MET A:99 , VAL A:103 , GLY A:163 , TRP A:164 , TYR A:406 , PHE A:412 , HIS A:413 , MET A:416 , SER A:417 , MET A:452 , PHE A:460 , GLN A:463 , ARG A:473 , ARG A:474 , SER A:496 , PHE A:500 , HOH A:583 , HOH A:618
BINDING SITE FOR RESIDUE HEA A 559
02
AC2
SOFTWARE
TRP A:164 , TRP A:272 , VAL A:279 , TYR A:280 , HIS A:325 , HIS A:326 , THR A:344 , THR A:351 , GLY A:352 , VAL A:355 , GLY A:387 , GLY A:390 , LEU A:393 , SER A:394 , ASP A:399 , HIS A:403 , VAL A:408 , HIS A:411 , PHE A:412 , VAL A:415 , MET A:416 , ARG A:473 , PER A:576 , HOH A:580 , HOH A:581
BINDING SITE FOR RESIDUE HEA A 560
03
AC3
SOFTWARE
HIS A:276 , HIS A:325 , HIS A:326 , PER A:576
BINDING SITE FOR RESIDUE CU A 561
04
AC4
SOFTWARE
HIS A:403 , ASP A:404 , HOH A:582 , HOH A:684 , GLU B:218 , HOH B:280
BINDING SITE FOR RESIDUE MG A 562
05
AC5
SOFTWARE
GLU A:56 , HIS A:59 , GLY A:61 , GLN A:63 , HOH A:669
BINDING SITE FOR RESIDUE CA A 563
06
AC6
SOFTWARE
TYR A:484 , LMT A:572 , LMT B:278
BINDING SITE FOR RESIDUE LDA A 564
07
AC7
SOFTWARE
MET A:55 , LEU A:72 , LMT A:571
BINDING SITE FOR RESIDUE LDA A 565
08
AC8
SOFTWARE
GLN A:336
BINDING SITE FOR RESIDUE LDA A 566
09
AC9
SOFTWARE
PHE A:37 , PHE A:512 , LMT A:570
BINDING SITE FOR RESIDUE LDA A 567
10
BC1
SOFTWARE
LEU A:447 , PHE A:502 , LMT A:569 , HOH A:660
BINDING SITE FOR RESIDUE LMT A 568
11
BC2
SOFTWARE
PRO A:441 , TRP A:443 , GLY A:505 , TYR A:509 , LMT A:568 , SER D:10
BINDING SITE FOR RESIDUE LMT A 569
12
BC3
SOFTWARE
ARG A:21 , LYS A:29 , MET A:435 , SER A:436 , ILE A:504 , PRO A:537 , LDA A:567
BINDING SITE FOR RESIDUE LMT A 570
13
BC4
SOFTWARE
HIS A:59 , TYR A:64 , ALA A:74 , TYR A:494 , LDA A:565 , HOH A:624
BINDING SITE FOR RESIDUE LMT A 571
14
BC5
SOFTWARE
MET A:451 , ILE A:491 , TYR A:494 , LDA A:564
BINDING SITE FOR RESIDUE LMT A 572
15
BC6
SOFTWARE
ILE B:57
BINDING SITE FOR RESIDUE LMT A 573
16
BC7
SOFTWARE
LEU A:342 , THR A:346 , VAL A:349 , VAL B:86 , LEU B:89 , VAL B:90
BINDING SITE FOR RESIDUE LMT A 574
17
BC8
SOFTWARE
MET A:24 , THR A:26 , ARG A:129 , ASN A:132
BINDING SITE FOR RESIDUE LMT A 575
18
BC9
SOFTWARE
HIS A:276 , VAL A:279 , HIS A:326 , HEA A:560 , CU A:561
BINDING SITE FOR RESIDUE PER A 576
19
CC1
SOFTWARE
CYS B:216 , GLU B:218 , CYS B:220 , HIS B:224 , CU B:271
BINDING SITE FOR RESIDUE CU B 270
20
CC2
SOFTWARE
HIS B:181 , CYS B:216 , CYS B:220 , MET B:227 , CU B:270
BINDING SITE FOR RESIDUE CU B 271
21
CC3
SOFTWARE
ARG A:468 , ASN B:19 , LDA B:275
BINDING SITE FOR RESIDUE LDA B 272
22
CC4
SOFTWARE
HIS B:36 , PHE B:37
BINDING SITE FOR RESIDUE LDA B 273
23
CC5
SOFTWARE
PHE A:356 , PHE B:48 , ILE B:77 , ILE B:80 , VAL B:84 , LMT B:279
BINDING SITE FOR RESIDUE LDA B 274
24
CC6
SOFTWARE
TYR B:40 , THR B:43 , LDA B:272
BINDING SITE FOR RESIDUE LDA B 275
25
CC7
SOFTWARE
ALA B:94 , LMT B:277 , LMT D:121
BINDING SITE FOR RESIDUE LDA B 276
26
CC8
SOFTWARE
LEU B:97 , PRO B:98 , PHE B:101 , ARG B:102 , GLU B:105 , LDA B:276
BINDING SITE FOR RESIDUE LMT B 277
27
CC9
SOFTWARE
PHE A:461 , TRP A:485 , LDA A:564 , ASN B:15 , GLY B:16 , HOH B:351
BINDING SITE FOR RESIDUE LMT B 278
28
DC1
SOFTWARE
PHE A:356 , LEU B:52 , PHE B:71 , HIS B:73 , ASN B:74 , TRP B:81 , LDA B:274
BINDING SITE FOR RESIDUE LMT B 279
29
DC2
SOFTWARE
TRP B:33 , LEU B:87 , VAL B:90 , PHE B:95 , ILE B:99 , LDA B:276 , GLU D:27 , ASN D:28 , TYR D:30
BINDING SITE FOR RESIDUE LMT D 121
[
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
(5, 5)
Info
All PROSITE Patterns/Profiles
1: COX1 (A:22-546)
2: COX2_TM (B:12-107)
3: COX2_CUA (B:109-245)
4: COX2 (B:179-227)
5: COX1_CUB (A:272-326)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1B_PARDE
22-550
1
A:22-546
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_PARDE
41-136
1
B:12-107
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_PARDE
138-274
1
B:109-245
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_PARDE
208-256
1
B:179-227
5
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1B_PARDE
272-326
1
A:272-326
[
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, 5)
Info
All SCOP Domains
1a: SCOP_d3ehbb1 (B:108-253)
2a: SCOP_d3ehbc_ (C:)
2b: SCOP_d3ehbd_ (D:)
3a: SCOP_d3ehba_ (A:)
4a: SCOP_d3ehbb2 (B:1-107)
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)
Paracoccus denitrificans [TaxId: 266]
(4)
1a
d3ehbb1
B:108-253
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Mouse (Mus musculus) [TaxId: 10090]
(112)
2a
d3ehbc_
C:
2b
d3ehbd_
D:
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
:
automated matches
(24)
Paracoccus denitrificans [TaxId: 266]
(2)
3a
d3ehba_
A:
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 aa3 type cytochrome c oxidase subunit II
(10)
Paracoccus denitrificans [TaxId: 266]
(4)
4a
d3ehbb2
B:1-107
[
close SCOP info
]
CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_3ehbB02 (B:25-105)
2a: CATH_3ehbA00 (A:17-546)
3a: CATH_3ehbB01 (B:1-24,B:106-253)
4a: CATH_3ehbD00 (D:1-109)
4b: CATH_3ehbC00 (C:1-119)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.90, no name defined]
(33)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
1a
3ehbB02
B:25-105
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Paracoccus denitrificans. Organism_taxid: 266.
(1)
2a
3ehbA00
A:17-546
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Paracoccus denitrificans. Organism_taxid: 266.
(3)
3a
3ehbB01
B:1-24,B:106-253
Homologous Superfamily
:
Immunoglobulins
(2282)
Paracoccus denitrificans. Organism_taxid: 266.
(2)
4a
3ehbD00
D:1-109
4b
3ehbC00
C:1-119
[
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
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 (198 KB)
Header - Asym.Unit
Biol.Unit 1 (186 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
3EHB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help