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.
2E74
Asym. Unit
Info
Asym.Unit (180 KB)
Biol.Unit 1 (327 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE CYTOCHROME B6F COMPLEX FROM M.LAMINOSUS
Authors
:
W. A. Cramer, E. Yamashita, H. Zhang
Date
:
05 Jan 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (2x)
Keywords
:
Photosynthesis, Cytochrome F, Rieske Iron-Sulfur Protein, Heme Cn
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Yamashita, H. Zhang, W. A. Cramer
Structure Of The Cytochrome B(6)F Complex: Quinone Analogue Inhibitors As Ligands Of Heme C(N)
J. Mol. Biol. V. 370 39 2007
[
close entry info
]
Hetero Components
(8, 16)
Info
All Hetero Components
1a: BETA-CAROTENE (BCRa)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
3a: CHLOROPHYLL A (CLAa)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
5d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
6a: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCa)
6b: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCb)
7a: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO... (SQDa)
8a: UNDECYL-MALTOSIDE (UMQa)
8b: UNDECYL-MALTOSIDE (UMQb)
8c: UNDECYL-MALTOSIDE (UMQc)
8d: UNDECYL-MALTOSIDE (UMQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCR
1
Ligand/Ion
BETA-CAROTENE
2
CD
2
Ligand/Ion
CADMIUM ION
3
CLA
1
Ligand/Ion
CHLOROPHYLL A
4
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
OPC
2
Ligand/Ion
(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
7
SQD
1
Ligand/Ion
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
8
UMQ
4
Ligand/Ion
UNDECYL-MALTOSIDE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:75 , HOH A:1105 , HIS C:143 , HOH C:302
BINDING SITE FOR RESIDUE CD A 1001
02
AC2
SOFTWARE
GLN A:47 , GLY A:51 , PHE A:52 , MET A:54 , TYR A:58 , ARG A:83 , HIS A:86 , ARG A:87 , ALA A:90 , MET A:93 , PHE A:131 , GLY A:135 , LEU A:138 , PRO A:139 , HIS A:187 , PHE A:189
BINDING SITE FOR RESIDUE HEM A 301
03
AC3
SOFTWARE
TYR A:34 , GLY A:37 , GLY A:38 , MET A:93 , HIS A:100 , VAL A:101 , ARG A:103 , VAL A:104 , GLY A:109 , ARG A:114 , THR A:117 , TRP A:118 , GLY A:121 , VAL A:122 , LEU A:124 , MET A:199 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:1106
BINDING SITE FOR RESIDUE HEM A 302
04
AC4
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , HOH A:1106 , ASN B:25 , VAL B:39 , PHE B:40 , ILE B:44
BINDING SITE FOR RESIDUE HEM A 303
05
AC5
SOFTWARE
GLU A:75 , PHE A:78 , TRP A:80 , LEU A:81 , VAL B:52 , ASN C:253 , ARG C:254 , TRP C:257 , PHE C:261 , PRO D:37
BINDING SITE FOR RESIDUE UMQ A 1101
06
AC6
SOFTWARE
LEU A:12 , LYS A:208
BINDING SITE FOR RESIDUE UMQ A 1102
07
AC7
SOFTWARE
ASN A:3 , TYR A:5 , ASP A:6 , ILE A:14 , GLN A:15 , UMQ A:1104
BINDING SITE FOR RESIDUE UMQ A 1103
08
AC8
SOFTWARE
THR A:22 , UMQ A:1103 , TRP B:32 , SQD D:201
BINDING SITE FOR RESIDUE UMQ A 1104
09
AC9
SOFTWARE
ASP B:58 , LYS C:146 , GLU F:4 , GLU G:3
BINDING SITE FOR RESIDUE CD B 161
10
BC1
SOFTWARE
ILE A:98 , PHE A:102 , TYR A:105 , TYR B:80 , PRO B:83 , VAL B:84 , ILE B:87 , MET B:101 , VAL B:104 , LEU B:108 , ILE B:132 , PHE B:133 , THR B:140 , OPC B:202 , HOH B:211
BINDING SITE FOR RESIDUE CLA B 201
11
BC2
SOFTWARE
LEU B:100 , SER B:103 , LEU B:108 , VAL B:111 , ILE B:114 , GLU B:115 , ASN B:118 , ARG B:126 , PRO B:127 , VAL B:128 , ALA B:129 , CLA B:201
BINDING SITE FOR RESIDUE OPC B 202
12
BC3
SOFTWARE
TYR C:1 , PRO C:2 , TRP C:4 , ALA C:5 , CYS C:22 , CYS C:25 , HIS C:26 , GLN C:60 , LEU C:70 , ASN C:71 , VAL C:72 , GLY C:73 , ALA C:74 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , ILE C:160 , TYR C:161
BINDING SITE FOR RESIDUE HEM C 301
13
BC4
SOFTWARE
CYS D:108 , HIS D:110 , CYS D:126 , CYS D:128 , HIS D:129 , SER D:131 , PRO D:143
BINDING SITE FOR RESIDUE FES D 200
14
BC5
SOFTWARE
UMQ A:1104 , TRP B:32 , TYR B:38 , LYS C:275 , ARG D:16 , ASN D:20 , LEU D:21 , GLY D:25
BINDING SITE FOR RESIDUE SQD D 201
15
BC6
SOFTWARE
ILE A:39 , MET A:96 , LEU A:99 , ILE F:16 , PHE F:17 , TRP F:20 , ALA G:16 , GLY G:19 , GLY G:20 , TYR G:23 , PHE H:15 , ILE H:19 , OPC H:1002
BINDING SITE FOR RESIDUE BCR G 101
16
BC7
SOFTWARE
MET A:92 , CYS B:50 , GLY E:4 , ALA E:5 , LEU F:11 , LEU G:5 , LEU G:9 , BCR G:101 , TRP H:8 , LEU H:12 , PHE H:15
BINDING SITE FOR RESIDUE OPC H 1002
[
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: CYTB_NTER (A:4-215)
2: CYTB_CTER (B:35-160)
3: RIESKE (D:61-162)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_NTER
PS51002
Cytochrome b/b6 N-terminal region profile.
CYB6_MASLA
4-215
1
A:4-215
2
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
PETD_MASLA
35-160
1
B:35-160
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_MASLA
61-162
1
D:61-162
[
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
(8, 8)
Info
All SCOP Domains
1a: SCOP_d2e74d1 (D:46-179)
2a: SCOP_d2e74b1 (B:1-160)
3a: SCOP_d2e74a_ (A:)
4a: SCOP_d2e74d2 (D:9-45)
5a: SCOP_d2e74g_ (G:)
6a: SCOP_d2e74e1 (E:1-32)
7a: SCOP_d2e74f_ (F:)
8a: SCOP_d2e74h_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
automated matches
(8)
Mastigocladus laminosus [TaxId: 83541]
(2)
1a
d2e74d1
D:46-179
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Superfamily
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Family
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(39)
Protein domain
:
Subunit IV of the cytochrome b6f complex
(8)
Mastigocladus laminosus [TaxId: 83541]
(7)
2a
d2e74b1
B:1-160
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Transmembrane di-heme cytochromes
(48)
Family
:
Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Protein domain
:
automated matches
(11)
Mastigocladus laminosus [TaxId: 83541]
(3)
3a
d2e74a_
A:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Mastigocladus laminosus [TaxId: 83541]
(2)
4a
d2e74d2
D:9-45
Superfamily
:
PetG subunit of the cytochrome b6f complex
(8)
Family
:
PetG subunit of the cytochrome b6f complex
(8)
Protein domain
:
automated matches
(3)
Mastigocladus laminosus [TaxId: 83541]
(3)
5a
d2e74g_
G:
Superfamily
:
PetL subunit of the cytochrome b6f complex
(7)
Family
:
PetL subunit of the cytochrome b6f complex
(7)
Protein domain
:
PetL subunit of the cytochrome b6f complex
(7)
Mastigocladus laminosus [TaxId: 83541]
(6)
6a
d2e74e1
E:1-32
Superfamily
:
PetM subunit of the cytochrome b6f complex
(9)
Family
:
PetM subunit of the cytochrome b6f complex
(9)
Protein domain
:
PetM subunit of the cytochrome b6f complex
(8)
Mastigocladus laminosus [TaxId: 83541]
(7)
7a
d2e74f_
F:
Superfamily
:
PetN subunit of the cytochrome b6f complex
(9)
Family
:
PetN subunit of the cytochrome b6f complex
(9)
Protein domain
:
automated matches
(4)
Mastigocladus laminosus [TaxId: 83541]
(3)
8a
d2e74h_
H:
[
close SCOP info
]
CATH Domains
(7, 7)
Info
all CATH domains
1a: CATH_2e74B01 (B:9-66)
2a: CATH_2e74B02 (B:67-160)
3a: CATH_2e74A00 (A:1-215)
4a: CATH_2e74C03 (C:255-288)
5a: CATH_2e74D02 (D:48-179)
6a: CATH_2e74C02 (C:172-233)
7a: CATH_2e74C01 (C:1-171,C:234-254)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome C Oxidase; Chain M
(30)
Homologous Superfamily
:
Cytochrome C Oxidase, chain M
(29)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
1a
2e74B01
B:9-66
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
plastocyanin oxidoreductase
(7)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
2a
2e74B02
B:67-160
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
3a
2e74A00
A:1-215
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(6)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
4a
2e74C03
C:255-288
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
5a
2e74D02
D:48-179
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
6a
2e74C02
C:172-233
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
7a
2e74C01
C:1-171,C:234-254
[
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
Chain E
Chain F
Chain G
Chain H
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 (180 KB)
Header - Asym.Unit
Biol.Unit 1 (327 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
2E74
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help