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.
1L9J
Biol. Unit 2
Info
Asym.Unit (329 KB)
Biol.Unit 1 (162 KB)
Biol.Unit 2 (161 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF THE CYTOCHROME-C(2)-PHOTOSYNTHETIC REACTION CENTER ELECTRON TRANSFER COMPLEX FROM RHODOBACTER SPHAEROIDES IN TYPE I CO-CRYSTALS
Authors
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Feher
Date
:
24 Mar 02 (Deposition) - 12 Jun 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.25
Chains
:
Asym. Unit : C,D,H,L,M,R,S,T
Biol. Unit 1: C,H,L,M (1x)
Biol. Unit 2: D,R,S,T (1x)
Keywords
:
Bacterial Photosynthesis, Electron Transfer Proteins, Protein-Protein Interactions, Membrane Proteins, Protein Complexes, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Fehe
X-Ray Structure Determination Of The Cytochrome C2: Reactio Center Electron Transfer Complex From Rhodobacter Sphaeroides.
J. Mol. Biol. V. 319 501 2002
[
close entry info
]
Hetero Components
(6, 11)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
1e: BACTERIOCHLOROPHYLL A (BCLe)
1f: BACTERIOCHLOROPHYLL A (BCLf)
1g: BACTERIOCHLOROPHYLL A (BCLg)
1h: BACTERIOCHLOROPHYLL A (BCLh)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
2c: BACTERIOPHEOPHYTIN A (BPHc)
2d: BACTERIOPHEOPHYTIN A (BPHd)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: FE (II) ION (FE2a)
4b: FE (II) ION (FE2b)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
6b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
6c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
6d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
7a: UBIQUINONE-10 (U10a)
7b: UBIQUINONE-10 (U10b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
FE2
1
Ligand/Ion
FE (II) ION
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
LDA
2
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
1
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: BC5 (SOFTWARE)
04: BC6 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
HIS R:190 , HIS R:230 , HIS S:219 , GLU S:234 , HIS S:266
BINDING SITE FOR RESIDUE FE2 S 2007
02
AC3
SOFTWARE
HIS S:145
BINDING SITE FOR RESIDUE CL S 2012
03
BC5
SOFTWARE
HIS R:168 , MET R:174 , ILE R:177 , SER R:178 , THR R:182 , ILE S:179 , HIS S:182 , LEU S:183 , THR S:186 , BCL S:2003 , LDA S:2011
BINDING SITE FOR RESIDUE BCL S 2001
04
BC6
SOFTWARE
PHE R:97 , ALA R:124 , TYR R:128 , LEU R:131 , VAL R:157 , TYR R:162 , PHE R:167 , HIS R:168 , HIS R:173 , ILE R:177 , PHE R:180 , SER R:244 , ALA R:245 , CYS R:247 , MET R:248 , BCL R:2004 , BCL S:2003 , BPH S:2006
BINDING SITE FOR RESIDUE BCL R 2002
05
BC7
SOFTWARE
VAL R:157 , TYR R:162 , PHE R:181 , BCL R:2002 , BPH R:2005 , TRP S:66 , ALA S:153 , LEU S:156 , TRP S:157 , ASN S:187 , PHE S:189 , SER S:190 , LEU S:196 , PHE S:197 , HIS S:202 , SER S:205 , ILE S:206 , LEU S:209 , TYR S:210 , GLY S:280 , ILE S:284 , BCL S:2001
BINDING SITE FOR RESIDUE BCL S 2003
06
BC8
SOFTWARE
ILE R:46 , ILE R:49 , TYR R:128 , LEU R:131 , PHE R:146 , ILE R:150 , TRP R:151 , HIS R:153 , LEU R:154 , BCL R:2002 , PHE S:197 , GLY S:203 , ILE S:206 , ALA S:207 , TYR S:210 , LEU S:214 , BPH S:2006 , LDA S:2010
BINDING SITE FOR RESIDUE BCL R 2004
07
BC9
SOFTWARE
PHE R:181 , ALA R:184 , LEU R:185 , LEU R:189 , LEU R:219 , SER S:59 , LEU S:60 , GLY S:63 , LEU S:64 , ALA S:125 , TRP S:129 , ALA S:149 , PHE S:150 , ALA S:153 , ALA S:273 , BCL S:2003
BINDING SITE FOR RESIDUE BPH R 2005
08
CC1
SOFTWARE
ALA R:42 , ILE R:49 , ALA R:93 , ALA R:96 , PHE R:97 , TRP R:100 , GLU R:104 , ILE R:117 , ALA R:120 , PHE R:121 , TYR R:128 , TYR R:148 , LEU R:238 , VAL R:241 , BCL R:2002 , BCL R:2004 , TYR S:210 , ALA S:213 , LEU S:214 , MET S:218 , TRP S:252 , MET S:256
BINDING SITE FOR RESIDUE BPH S 2006
09
CC2
SOFTWARE
TRP R:100 , HIS S:219 , THR S:222 , ALA S:249 , TRP S:252 , PHE S:258 , ASN S:259 , ALA S:260 , THR S:261 , MET S:262 , TRP S:268
BINDING SITE FOR RESIDUE U10 S 2008
10
CC3
SOFTWARE
CYS D:15 , CYS D:18 , HIS D:19 , THR D:36 , PRO D:38 , ARG D:46 , ALA D:48 , GLY D:49 , PHE D:54 , TYR D:57 , GLY D:58 , MET D:61 , TRP D:71 , PHE D:76 , TYR D:79 , LYS D:99 , MET D:100 , THR D:101 , PHE D:102
BINDING SITE FOR RESIDUE HEM D 2009
11
CC4
SOFTWARE
BCL R:2004 , PRO S:200 , LEU S:204 , PHE S:208 , ILE T:28
BINDING SITE FOR RESIDUE LDA S 2010
12
CC5
SOFTWARE
PHE S:74 , MET S:122 , VAL S:175 , PRO S:176 , GLY S:178 , HIS S:182 , BCL S:2001
BINDING SITE FOR RESIDUE LDA S 2011
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: CYTC (D:3-121)
2: REACTION_CENTER (S:195-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CYC2_RHOSH
3-121
1
-
D:3-121
CYC2_RHOS4
24-142
1
-
D:3-121
2
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOS4
167-193
1
-
R:166-192
RCEL_RHOSH
167-193
1
-
R:166-192
RCEM_RHOS4
196-222
1
-
S:195-221
RCEM_RHOSH
196-222
1
-
S:195-221
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1l9jc_ (C:)
1b: SCOP_d1l9jd_ (D:)
2a: SCOP_d1l9jh1 (H:36-253)
2b: SCOP_d1l9jt1 (T:36-253)
3a: SCOP_d1l9jl_ (L:)
3b: SCOP_d1l9jr_ (R:)
4a: SCOP_d1l9jm_ (M:)
4b: SCOP_d1l9js_ (S:)
5a: SCOP_d1l9jh2 (H:8-35)
5b: SCOP_d1l9jt2 (T:8-35)
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
:
Cytochrome c2
(21)
Rhodobacter sphaeroides [TaxId: 1063]
(5)
1a
d1l9jc_
C:
1b
d1l9jd_
D:
Class
:
All beta proteins
(24004)
Fold
:
PRC-barrel domain
(113)
Superfamily
:
PRC-barrel domain
(113)
Family
:
Photosynthetic reaction centre, H-chain, cytoplasmic domain
(108)
Protein domain
:
Photosynthetic reaction centre
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
2a
d1l9jh1
H:36-253
2b
d1l9jt1
T:36-253
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Superfamily
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Family
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Protein domain
:
L (light) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1l9jl_
L:
3b
d1l9jr_
R:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
4a
d1l9jm_
M:
4b
d1l9js_
S:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Protein domain
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
5a
d1l9jh2
H:8-35
5b
d1l9jt2
T:8-35
[
close SCOP info
]
CATH Domains
(4, 14)
Info
all CATH domains
1a: CATH_1l9jH02 (H:117-248)
1b: CATH_1l9jT02 (T:117-248)
2a: CATH_1l9jH01 (H:12-116)
2b: CATH_1l9jT01 (T:12-116)
3a: CATH_1l9jC00 (C:1-124)
3b: CATH_1l9jD00 (D:1-124)
4a: CATH_1l9jM02 (M:144-301)
4b: CATH_1l9jM01 (M:35-143)
4c: CATH_1l9jS01 (S:35-143)
4d: CATH_1l9jS02 (S:144-301)
4e: CATH_1l9jL01 (L:1-163)
4f: CATH_1l9jR01 (R:1-163)
4g: CATH_1l9jL02 (L:164-263)
4h: CATH_1l9jR02 (R:164-263)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 2
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 2
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
1a
1l9jH02
H:117-248
1b
1l9jT02
T:117-248
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 1
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 1
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
2a
1l9jH01
H:12-116
2b
1l9jT01
T:12-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
3a
1l9jC00
C:1-124
3b
1l9jD00
D:1-124
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
4a
1l9jM02
M:144-301
4b
1l9jM01
M:35-143
4c
1l9jS01
S:35-143
4d
1l9jS02
S:144-301
4e
1l9jL01
L:1-163
4f
1l9jR01
R:1-163
4g
1l9jL02
L:164-263
4h
1l9jR02
R:164-263
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_PRC_1l9jT01 (T:141-212)
1b: PFAM_PRC_1l9jT02 (T:141-212)
2a: PFAM_PRCH_1l9jT03 (T:8-137)
2b: PFAM_PRCH_1l9jT04 (T:8-137)
3a: PFAM_Photo_RC_1l9jR01 (R:29-272)
3b: PFAM_Photo_RC_1l9jR02 (R:29-272)
3c: PFAM_Photo_RC_1l9jS01 (S:50-301)
3d: PFAM_Photo_RC_1l9jS02 (S:50-301)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1l9jT01
T:141-212
1b
PRC-1l9jT02
T:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1l9jT03
T:8-137
2b
PRCH-1l9jT04
T:8-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1l9jR01
R:29-272
3b
Photo_RC-1l9jR02
R:29-272
3c
Photo_RC-1l9jS01
S:50-301
3d
Photo_RC-1l9jS02
S:50-301
[
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 D
Chain R
Chain S
Chain T
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 (329 KB)
Header - Asym.Unit
Biol.Unit 1 (162 KB)
Header - Biol.Unit 1
Biol.Unit 2 (161 KB)
Header - Biol.Unit 2
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
1L9J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help