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.
3O1Y
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (24 KB)
Biol.Unit 2 (25 KB)
Biol.Unit 3 (24 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ELECTRON TRANSFER COMPLEXES: EXPERIMENTAL MAPPING OF THE REDOX-DEPENDENT CYTOCHROME C ELECTROSTATIC SURFACE
Authors
:
M. De March, R. De Zorzi, N. Demitri, C. Gabbiani, A. Guerri, A. Casini L. Messori, S. Geremia
Date
:
22 Jul 10 (Deposition) - 25 Jan 12 (Release) - 25 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Cytochrome C, Globular Protein, Electron Transport Chain, Electron Carrier, Mitochondrial Respiration, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. De March, R. De Zorzi, N. Demitri, C. Gabbiani, A. Guerri, A. Casini, L. Messori, S. Geremia
Hold For Pubblication
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 28)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
1c: ACETYL GROUP (ACEc)
2a: HEME C (HECa)
2b: HEME C (HECb)
2c: HEME C (HECc)
3a: NITRATE ION (NO3a)
3b: NITRATE ION (NO3b)
3c: NITRATE ION (NO3c)
3d: NITRATE ION (NO3d)
3e: NITRATE ION (NO3e)
3f: NITRATE ION (NO3f)
3g: NITRATE ION (NO3g)
3h: NITRATE ION (NO3h)
3i: NITRATE ION (NO3i)
3j: NITRATE ION (NO3j)
3k: NITRATE ION (NO3k)
3l: NITRATE ION (NO3l)
3m: NITRATE ION (NO3m)
3n: NITRATE ION (NO3n)
3o: NITRATE ION (NO3o)
3p: NITRATE ION (NO3p)
3q: NITRATE ION (NO3q)
3r: NITRATE ION (NO3r)
3s: NITRATE ION (NO3s)
3t: NITRATE ION (NO3t)
3u: NITRATE ION (NO3u)
3v: NITRATE ION (NO3v)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
3
Mod. Amino Acid
ACETYL GROUP
2
HEC
3
Ligand/Ion
HEME C
3
NO3
22
Ligand/Ion
NITRATE 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
LYS A:13 , CYS A:14 , GLN A:16 , CYS A:17 , HIS A:18 , THR A:28 , GLY A:29 , PRO A:30 , THR A:40 , GLY A:41 , TYR A:48 , THR A:49 , ASN A:52 , TRP A:59 , TYR A:67 , THR A:78 , LYS A:79 , MET A:80 , ILE A:81 , PHE A:82 , HOH A:125 , HOH A:133 , HOH B:135
BINDING SITE FOR RESIDUE HEC A 105
02
AC2
SOFTWARE
GLU A:4 , LYS A:7 , LYS C:72 , ALA C:83
BINDING SITE FOR RESIDUE NO3 A 106
03
AC3
SOFTWARE
LYS A:8 , LYS C:13 , GLY C:84 , ILE C:85 , LYS C:86 , HOH C:138 , HOH C:207
BINDING SITE FOR RESIDUE NO3 A 107
04
AC4
SOFTWARE
LYS A:8 , VAL A:11 , GLN A:12 , PHE C:82 , ALA C:83 , GLY C:84 , HOH C:207
BINDING SITE FOR RESIDUE NO3 A 108
05
AC5
SOFTWARE
LYS A:13 , HOH A:276 , HOH A:413 , GLN B:12 , NO3 B:107
BINDING SITE FOR RESIDUE NO3 A 109
06
AC6
SOFTWARE
THR A:19 , VAL A:20 , GLU A:21 , HOH A:148 , HOH A:164 , HOH A:301 , HOH A:515 , THR C:28 , ILE C:81
BINDING SITE FOR RESIDUE NO3 A 110
07
AC7
SOFTWARE
PHE A:36 , LYS A:99 , ASN A:103 , HOH A:156
BINDING SITE FOR RESIDUE NO3 A 111
08
AC8
SOFTWARE
PHE A:82 , ALA A:83 , GLY A:84 , HOH A:138 , LYS B:8 , VAL B:11 , GLN B:12
BINDING SITE FOR RESIDUE NO3 A 112
09
AC9
SOFTWARE
GLU A:4 , LYS A:5 , LYS A:8 , HOH A:356 , HOH A:463 , HOH A:482
BINDING SITE FOR RESIDUE NO3 A 113
10
BC1
SOFTWARE
LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , THR B:28 , GLY B:29 , PRO B:30 , THR B:40 , GLY B:41 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , TYR B:67 , THR B:78 , LYS B:79 , MET B:80 , ILE B:81 , PHE B:82 , LEU B:94 , HOH B:152 , HOH B:160
BINDING SITE FOR RESIDUE HEC B 105
11
BC2
SOFTWARE
LYS A:72 , ALA A:83 , GLU B:4 , LYS B:7 , HOH B:411
BINDING SITE FOR RESIDUE NO3 B 106
12
BC3
SOFTWARE
LYS A:13 , GLY A:84 , ILE A:85 , LYS A:86 , NO3 A:109 , HOH A:138 , LYS B:8 , HOH B:131 , HOH B:277
BINDING SITE FOR RESIDUE NO3 B 107
13
BC4
SOFTWARE
LYS B:13 , GLY B:84 , ILE B:85 , LYS B:86 , HOH B:141 , HOH B:326 , HOH B:490 , LYS C:8
BINDING SITE FOR RESIDUE NO3 B 108
14
BC5
SOFTWARE
THR A:28 , ILE A:81 , PHE B:10 , THR B:19 , VAL B:20 , GLU B:21 , HOH B:127 , HOH B:135 , HOH B:245
BINDING SITE FOR RESIDUE NO3 B 109
15
BC6
SOFTWARE
GLU B:4 , LYS B:5 , LYS B:8 , HOH B:362 , HOH B:373
BINDING SITE FOR RESIDUE NO3 B 110
16
BC7
SOFTWARE
GLY B:45 , PHE B:46 , THR B:47 , HOH B:123 , HOH B:140 , HOH B:169 , HOH B:511
BINDING SITE FOR RESIDUE NO3 B 111
17
BC8
SOFTWARE
PHE B:82 , ALA B:83 , GLY B:84 , HOH B:203 , HOH B:518 , LYS C:8 , VAL C:11
BINDING SITE FOR RESIDUE NO3 B 112
18
BC9
SOFTWARE
PHE B:36 , GLY B:37 , HOH B:210 , HOH B:352 , PHE C:36 , LYS C:60 , GLU C:61 , LYS C:99 , HOH C:273 , HOH C:408
BINDING SITE FOR RESIDUE NO3 B 113
19
CC1
SOFTWARE
VAL A:11 , HOH A:515 , LYS C:13 , CYS C:14 , GLN C:16 , CYS C:17 , HIS C:18 , THR C:28 , GLY C:29 , PRO C:30 , THR C:40 , GLY C:41 , TYR C:48 , THR C:49 , ASN C:52 , TRP C:59 , TYR C:67 , THR C:78 , LYS C:79 , MET C:80 , ILE C:81 , PHE C:82 , LEU C:94 , HOH C:145 , HOH C:155
BINDING SITE FOR RESIDUE HEC C 105
20
CC2
SOFTWARE
LYS B:72 , ALA B:83 , HOH B:146 , GLU C:4 , LYS C:7 , HOH C:521
BINDING SITE FOR RESIDUE NO3 C 106
21
CC3
SOFTWARE
GLN A:12 , GLN C:12 , LYS C:13
BINDING SITE FOR RESIDUE NO3 C 107
22
CC4
SOFTWARE
THR B:28 , ILE B:81 , HOH B:155 , HOH B:289 , PHE C:10 , THR C:19 , VAL C:20 , GLU C:21
BINDING SITE FOR RESIDUE NO3 C 108
23
CC5
SOFTWARE
PHE B:36 , LYS B:99 , ASN B:103 , HOH B:352 , PHE C:36 , LYS C:99 , ASN C:103
BINDING SITE FOR RESIDUE NO3 C 109
24
CC6
SOFTWARE
PHE B:36 , LYS B:60 , GLU B:61 , GLU B:62 , LYS B:99 , HOH B:398 , PHE C:36 , GLY C:37 , HOH C:132 , HOH C:164
BINDING SITE FOR RESIDUE NO3 C 110
25
CC7
SOFTWARE
MET B:65 , GLU B:66 , GLU B:69 , ARG B:91 , HOH B:180 , HOH B:328 , LYS C:88
BINDING SITE FOR RESIDUE NO3 C 111
[
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
(1, 3)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:1-102,B:1-102,C:1-102)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CYC_HORSE
2-103
3
A:1-102
B:1-102
C:1-102
[
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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3o1ya_ (A:)
1b: SCOP_d3o1yb_ (B:)
1c: SCOP_d3o1yc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
Mitochondrial cytochrome c
(81)
Horse (Equus caballus) [TaxId: 9796]
(21)
1a
d3o1ya_
A:
1b
d3o1yb_
B:
1c
d3o1yc_
C:
[
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 (77 KB)
Header - Asym.Unit
Biol.Unit 1 (24 KB)
Header - Biol.Unit 1
Biol.Unit 2 (25 KB)
Header - Biol.Unit 2
Biol.Unit 3 (24 KB)
Header - Biol.Unit 3
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
3O1Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
