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.
1OFY
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (118 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THREE DIMENSIONAL STRUCTURE OF THE REDUCED FORM OF NINE-HEME CYTOCHROME C AT PH 7.5
Authors
:
I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Date
:
22 Apr 03 (Deposition) - 18 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Multiheme Cytochrome C, Electron Transport, Electron Transfer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Redox-Bohr And Other Cooperativity Effects In The Nine-Heme Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774: Crystallographic And Modeling Studies
J. Biol. Chem. V. 278 36455 2003
[
close entry info
]
Hetero Components
(3, 21)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: HEME C (HECa)
3b: HEME C (HECb)
3c: HEME C (HECc)
3d: HEME C (HECd)
3e: HEME C (HECe)
3f: HEME C (HECf)
3g: HEME C (HECg)
3h: HEME C (HECh)
3i: HEME C (HECi)
3j: HEME C (HECj)
3k: HEME C (HECk)
3l: HEME C (HECl)
3m: HEME C (HECm)
3n: HEME C (HECn)
3o: HEME C (HECo)
3p: HEME C (HECp)
3q: HEME C (HECq)
3r: HEME C (HECr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
HEC
18
Ligand/Ion
HEME C
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:122 , GLU A:124 , HOH A:2263 , LYS B:121 , SER B:232 , PRO B:233
BINDING SITE FOR RESIDUE ACT A1302
02
AC2
SOFTWARE
SER A:8 , ALA A:10 , ILE A:14 , PHE A:35 , HIS A:37 , CYS A:47 , CYS A:50 , HIS A:51 , PRO A:56 , SER A:58 , HEC A:1295 , HOH A:2011 , HOH A:2049 , HOH A:2243 , HOH A:2244 , HOH A:2245
BINDING SITE FOR RESIDUE HEC A1293
03
AC3
SOFTWARE
CYS A:50 , HIS A:52 , THR A:53 , VAL A:57 , CYS A:59 , THR A:61 , CYS A:62 , HIS A:63 , GLU A:70 , GLY A:71 , ASN A:72 , ARG A:78 , ALA A:79 , MET A:80 , ARG A:88 , PRO A:94 , VAL A:95 , HOH A:2246
BINDING SITE FOR RESIDUE HEC A1294
04
AC4
SOFTWARE
VAL A:33 , PHE A:35 , ASN A:36 , ILE A:39 , HIS A:40 , LYS A:43 , VAL A:95 , SER A:96 , CYS A:97 , CYS A:100 , HIS A:101 , GLN A:104 , LYS A:212 , LEU A:213 , ALA A:216 , HEC A:1293 , HEC A:1297 , HOH A:2247 , HOH A:2248 , HOH A:2249 , HOH A:2250
BINDING SITE FOR RESIDUE HEC A1295
05
AC5
SOFTWARE
GLU A:102 , THR A:105 , ARG A:108 , GLU A:110 , CYS A:111 , CYS A:114 , HIS A:115 , VAL A:118 , PRO A:120 , LYS A:121 , TRP A:126 , ASP A:211 , PHE A:217 , HIS A:218 , ILE A:223 , THR A:227 , HOH A:2091 , HOH A:2105 , HOH A:2251 , HOH A:2252
BINDING SITE FOR RESIDUE HEC A1296
06
AC6
SOFTWARE
MET A:16 , PHE A:17 , PRO A:18 , ALA A:29 , MET A:30 , LYS A:31 , VAL A:33 , LEU A:76 , MET A:80 , HIS A:81 , CYS A:97 , TRP A:126 , CYS A:127 , CYS A:130 , HIS A:131 , HEC A:1295 , HOH A:2253 , HOH A:2254 , ARG B:231 , PRO B:239 , SER B:243
BINDING SITE FOR RESIDUE HEC A1297
07
AC7
SOFTWARE
ALA A:177 , PRO A:178 , PHE A:195 , HIS A:197 , LEU A:201 , LEU A:224 , CYS A:225 , CYS A:228 , HIS A:229 , LEU A:236 , LYS A:240 , CYS A:241 , TYR A:263 , HEC A:1300 , HOH A:2256 , LYS B:26
BINDING SITE FOR RESIDUE HEC A1298
08
AC8
SOFTWARE
CYS A:228 , HIS A:230 , ARG A:231 , LYS A:240 , CYS A:241 , CYS A:244 , HIS A:245 , GLY A:255 , ARG A:256 , PRO A:257 , ALA A:262 , LEU A:265 , GLN A:266 , HOH A:2103 , HOH A:2257 , GOL B:1302
BINDING SITE FOR RESIDUE HEC A1299
09
AC9
SOFTWARE
ILE A:183 , SER A:193 , PHE A:195 , ARG A:199 , HIS A:200 , SER A:203 , LEU A:204 , ARG A:207 , GLN A:266 , CYS A:267 , CYS A:270 , HIS A:271 , MET A:274 , VAL A:276 , ARG A:278 , PRO A:279 , HEC A:1298 , HOH A:2258 , HOH A:2259 , HOH A:2260
BINDING SITE FOR RESIDUE HEC A1300
10
BC1
SOFTWARE
ILE A:183 , ASP A:184 , ALA A:185 , LEU A:186 , ALA A:187 , ASP A:188 , LYS A:189 , TYR A:190 , TYR A:263 , HIS A:264 , MET A:268 , HIS A:271 , ASP A:281 , ASP A:283 , CYS A:284 , CYS A:287 , HIS A:288 , HOH A:2261 , HOH A:2262
BINDING SITE FOR RESIDUE HEC A1301
11
BC2
SOFTWARE
SER B:8 , ALA B:10 , ILE B:14 , MET B:16 , PHE B:35 , HIS B:37 , ILE B:44 , CYS B:47 , CYS B:50 , HIS B:51 , PRO B:56 , SER B:58 , HEC B:1295 , HOH B:2222 , HOH B:2223
BINDING SITE FOR RESIDUE HEC B1293
12
BC3
SOFTWARE
CYS B:50 , HIS B:52 , THR B:53 , VAL B:57 , CYS B:59 , THR B:61 , CYS B:62 , HIS B:63 , GLU B:70 , ARG B:78 , ALA B:79 , MET B:80 , ARG B:88 , PRO B:94 , VAL B:95 , HOH B:2094
BINDING SITE FOR RESIDUE HEC B1294
13
BC4
SOFTWARE
VAL B:33 , PHE B:35 , ASN B:36 , HIS B:40 , LYS B:43 , SER B:96 , CYS B:97 , CYS B:100 , HIS B:101 , GLN B:104 , LYS B:212 , LEU B:213 , ALA B:216 , HEC B:1293 , HOH B:2225 , HOH B:2226 , HOH B:2227 , HOH B:2228
BINDING SITE FOR RESIDUE HEC B1295
14
BC5
SOFTWARE
GLU B:102 , THR B:105 , ARG B:108 , GLU B:110 , CYS B:111 , CYS B:114 , HIS B:115 , LYS B:121 , TRP B:126 , ILE B:208 , ASP B:211 , PHE B:217 , HIS B:218 , ILE B:223 , THR B:227 , HOH B:2118 , HOH B:2229 , HOH B:2230
BINDING SITE FOR RESIDUE HEC B1296
15
BC6
SOFTWARE
ARG A:231 , PRO A:239 , SER A:243 , GOL A:1303 , MET B:16 , PHE B:17 , PRO B:18 , ALA B:29 , MET B:30 , LYS B:31 , PRO B:32 , LEU B:76 , MET B:80 , HIS B:81 , CYS B:97 , TRP B:126 , CYS B:127 , CYS B:130 , HIS B:131 , GOL B:1302 , HOH B:2039 , HOH B:2042
BINDING SITE FOR RESIDUE HEC B1297
16
BC7
SOFTWARE
LYS A:26 , HOH A:2019 , HOH A:2020 , ALA B:177 , PRO B:178 , HIS B:197 , LEU B:201 , LEU B:224 , CYS B:225 , CYS B:228 , HIS B:229 , LEU B:236 , LYS B:240 , CYS B:241 , TYR B:263 , HEC B:1300 , HOH B:2231 , HOH B:2232
BINDING SITE FOR RESIDUE HEC B1298
17
BC8
SOFTWARE
CYS B:228 , HIS B:230 , ARG B:231 , LYS B:240 , CYS B:241 , CYS B:244 , HIS B:245 , PRO B:257 , ALA B:262 , LEU B:265 , GLN B:266 , HOH B:2233 , HOH B:2234 , HOH B:2235
BINDING SITE FOR RESIDUE HEC B1299
18
BC9
SOFTWARE
CYS B:114 , ILE B:183 , SER B:193 , PHE B:195 , THR B:196 , ARG B:199 , HIS B:200 , SER B:203 , ARG B:207 , CYS B:267 , CYS B:270 , HIS B:271 , MET B:274 , VAL B:276 , PRO B:279 , HEC B:1298 , HOH B:2236 , HOH B:2237 , HOH B:2238 , HOH B:2239
BINDING SITE FOR RESIDUE HEC B1300
19
CC1
SOFTWARE
ILE B:183 , ASP B:184 , ALA B:185 , LEU B:186 , ALA B:187 , ASP B:188 , LYS B:189 , TYR B:190 , MET B:260 , TYR B:263 , HIS B:264 , CYS B:267 , MET B:268 , ARG B:280 , CYS B:284 , CYS B:287 , HIS B:288 , HOH B:2240 , HOH B:2241
BINDING SITE FOR RESIDUE HEC B1301
20
CC2
SOFTWARE
SER A:232 , PRO A:233 , HOH A:2192 , ARG B:122 , GLU B:124 , CYS B:127 , HEC B:1297 , HOH B:2117
BINDING SITE FOR RESIDUE GOL A1303
21
CC3
SOFTWARE
ARG A:256 , HEC A:1299 , ASP B:77 , HIS B:81 , HEC B:1297 , HOH B:2091 , HOH B:2242
BINDING SITE FOR RESIDUE GOL B1302
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:42-293,B:42-293)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
CYC9_DESDA
72-323
2
A:42-293
B:42-293
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d1ofya_ (A:)
1b: SCOP_d1ofyb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Cytochrome c3-like
(70)
Protein domain
:
Nine-heme cytochrome c
(4)
Desulfovibrio desulfuricans, ATCC 27774 [TaxId: 876]
(3)
1a
d1ofya_
A:
1b
d1ofyb_
B:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ofyA02 (A:1-99,A:130-167)
1b: CATH_1ofyA01 (A:100-129,A:168-292)
1c: CATH_1ofyB01 (B:100-129,B:168-292)
1d: CATH_1ofyB02 (B:1-99,B:130-167)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Cytochrome C3
(62)
Homologous Superfamily
:
Cytochrome C3
(62)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(8)
1a
1ofyA02
A:1-99,A:130-167
1b
1ofyA01
A:100-129,A:168-292
1c
1ofyB01
B:100-129,B:168-292
1d
1ofyB02
B:1-99,B:130-167
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_CIII_1ofyB01 (B:180-290)
1b: PFAM_Cytochrom_CIII_1ofyB02 (B:180-290)
1c: PFAM_Cytochrom_CIII_1ofyB03 (B:180-290)
1d: PFAM_Cytochrom_CIII_1ofyB04 (B:180-290)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Multiheme_cytos
(34)
Family
:
Cytochrom_CIII
(23)
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
(3)
1a
Cytochrom_CIII-1ofyB01
B:180-290
1b
Cytochrom_CIII-1ofyB02
B:180-290
1c
Cytochrom_CIII-1ofyB03
B:180-290
1d
Cytochrom_CIII-1ofyB04
B:180-290
[
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
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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (118 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
1OFY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help