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.
4I7Z
Asym. Unit
Info
Asym.Unit (449 KB)
Biol.Unit 1 (865 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 CYTOCHROME B6F IN DOPG, WITH DISORDERED RIESKE IRON-SULFUR PROTEIN SOLUBLE DOMAIN
Authors
:
S. S. Hasan, J. T. Stofleth, E. Yamashita, W. A. Cramer
Date
:
01 Dec 12 (Deposition) - 17 Apr 13 (Release) - 04 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (2x)
Keywords
:
Cytochrome, Membrane Protein, Plastoquinol:Plastocyanin Oxidoreductase, Plastocyanin, Thylakoid Membrane, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. S. Hasan, J. T. Stofleth, E. Yamashita, W. A. Cramer
Lipid-Induced Conformational Changes Within The Cytochrome B6F Complex Of Oxygenic Photosynthesis.
Biochemistry V. 52 2649 2013
[
close entry info
]
Hetero Components
(10, 19)
Info
All Hetero Components
01a: (2S)-3-(ACETYLOXY)-2-HYDROXYPROPYL... (1E2a)
02a: OCTADECANE (8K6a)
03a: BETA-CAROTENE (BCRa)
04a: CADMIUM ION (CDa)
04b: CADMIUM ION (CDb)
04c: CADMIUM ION (CDc)
05a: CHLOROPHYLL A (CLAa)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
06b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
06c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
06d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
07a: PENTADECANE (MYSa)
08a: N-OCTANE (OCTa)
09a: (2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYP... (OZ2a)
09b: (2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYP... (OZ2b)
09c: (2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYP... (OZ2c)
10a: UNDECYL-MALTOSIDE (UMQa)
10b: UNDECYL-MALTOSIDE (UMQb)
10c: UNDECYL-MALTOSIDE (UMQc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1E2
1
Ligand/Ion
(2S)-3-(ACETYLOXY)-2-HYDROXYPROPYL 6-DEOXY-6-SULFO-BETA-D-GLUCOPYRANOSIDE
2
8K6
1
Ligand/Ion
OCTADECANE
3
BCR
1
Ligand/Ion
BETA-CAROTENE
4
CD
3
Ligand/Ion
CADMIUM ION
5
CLA
1
Ligand/Ion
CHLOROPHYLL A
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
MYS
1
Ligand/Ion
PENTADECANE
8
OCT
1
Ligand/Ion
N-OCTANE
9
OZ2
3
Ligand/Ion
(2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6Z)-TRIDEC-6-ENOYLOXY]PROPYL (9Z)-OCTADEC-9-ENOATE
10
UMQ
3
Ligand/Ion
UNDECYL-MALTOSIDE
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:47 , PHE A:48 , GLY A:51 , PHE A:52 , MET A:54 , TYR A:58 , ARG A:83 , HIS A:86 , ARG A:87 , ALA A:90 , THR A:128 , 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
02
AC2
SOFTWARE
TYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , 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 , MET A:199 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:303 , HOH A:401 , HOH A:402 , HOH A:403
BINDING SITE FOR RESIDUE HEM A 302
03
AC3
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , THR A:42 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:302 , HOH A:401 , ASN B:25 , ASP B:35 , PHE B:40 , ILE B:44 , ARG H:26
BINDING SITE FOR RESIDUE HEM A 303
04
AC4
SOFTWARE
LEU A:169 , ALA A:186
BINDING SITE FOR RESIDUE MYS A 304
05
AC5
SOFTWARE
PHE A:52 , MET A:199
BINDING SITE FOR RESIDUE 8K6 A 305
06
AC6
SOFTWARE
LEU A:12 , GLU A:13 , ALA A:16 , LEU A:17 , ILE A:119 , LEU A:204 , LYS A:208
BINDING SITE FOR RESIDUE UMQ A 306
07
AC7
SOFTWARE
TYR A:5 , ASP A:6 , ILE A:14 , GLN A:15 , ALA A:18 , UMQ A:308
BINDING SITE FOR RESIDUE UMQ A 307
08
AC8
SOFTWARE
ALA A:18 , UMQ A:307 , GLU C:286 , 1E2 D:201
BINDING SITE FOR RESIDUE UMQ A 308
09
AC9
SOFTWARE
GLU A:75 , HIS C:143 , HOH C:401
BINDING SITE FOR RESIDUE CD A 309
10
BC1
SOFTWARE
TYR A:105 , ALA A:125 , VAL A:129 , TYR B:80 , PRO B:83 , VAL B:84 , ILE B:87 , MET B:101 , ILE B:132 , PHE B:133 , GLY B:136 , VAL B:139 , THR B:140 , OZ2 B:203 , HOH B:301 , HOH B:302
BINDING SITE FOR RESIDUE CLA B 201
11
BC2
SOFTWARE
ASP B:58 , LYS C:146 , GLU F:4 , GLU G:3
BINDING SITE FOR RESIDUE CD B 202
12
BC3
SOFTWARE
TYR A:105 , SER B:103 , GLU B:115 , ASN B:118 , ARG B:126 , VAL B:128 , ALA B:129 , CLA B:201
BINDING SITE FOR RESIDUE OZ2 B 203
13
BC4
SOFTWARE
TYR C:1 , 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
14
BC5
SOFTWARE
HIS C:150
BINDING SITE FOR RESIDUE CD C 302
15
BC6
SOFTWARE
PHE A:78 , TRP A:80 , ASN C:253 , TRP C:257
BINDING SITE FOR RESIDUE OZ2 C 303
16
BC7
SOFTWARE
UMQ A:308 , TRP B:32 , PRO B:33 , TYR B:38 , LYS C:275 , VAL C:279 , ARG D:16 , ASN D:20 , PHE D:24
BINDING SITE FOR RESIDUE 1E2 D 201
17
BC8
SOFTWARE
ILE A:32 , PHE A:33 , ILE A:39 , MET A:96 , LEU A:99 , ILE F:16 , PHE F:17 , ALA G:16 , GLY G:19 , GLY G:20 , TYR G:23 , OZ2 G:102 , ILE H:19
BINDING SITE FOR RESIDUE BCR G 101
18
BC9
SOFTWARE
MET A:92 , PRO C:37 , GLN C:38 , TYR E:8 , TYR F:7 , LEU G:5 , LEU G:9 , BCR G:101 , TRP H:8 , LEU H:12 , PHE H:15
BINDING SITE FOR RESIDUE OZ2 G 102
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(9, 9)
Info
All SCOP Domains
1a: SCOP_d4i7zc2 (C:170-231)
2a: SCOP_d4i7zc1 (C:1-169,C:232-249)
3a: SCOP_d4i7zb_ (B:)
4a: SCOP_d4i7za_ (A:)
5a: SCOP_d4i7zc3 (C:250-288)
6a: SCOP_d4i7zg_ (G:)
7a: SCOP_d4i7ze_ (E:)
8a: SCOP_d4i7zf_ (F:)
9a: SCOP_d4i7zh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Rudiment single hybrid motif
(69)
Family
:
Cytochrome f, small domain
(12)
Protein domain
:
Cytochrome f, small domain
(12)
Mastigocladus laminosus [TaxId: 83541]
(2)
1a
d4i7zc2
C:170-231
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Cytochrome f, large domain
(12)
Family
:
Cytochrome f, large domain
(12)
Protein domain
:
Cytochrome f, large domain
(12)
Mastigocladus laminosus [TaxId: 83541]
(2)
2a
d4i7zc1
C:1-169,C:232-249
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)
3a
d4i7zb_
B:
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)
4a
d4i7za_
A:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Family
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Protein domain
:
Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor
(3)
Mastigocladus laminosus [TaxId: 83541]
(2)
5a
d4i7zc3
C:250-288
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)
6a
d4i7zg_
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)
7a
d4i7ze_
E:
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)
8a
d4i7zf_
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)
9a
d4i7zh_
H:
[
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
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 (449 KB)
Header - Asym.Unit
Biol.Unit 1 (865 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
4I7Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
