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4H13
Asym. Unit
Info
Asym.Unit (347 KB)
Biol.Unit 1 (653 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CYTOCHROME B6F COMPLEX FROM MASTIGOCLADUS LAMINOSUS WITH TDS
Authors
:
S. S. Hasan, E. Yamashita, D. Baniulis, W. A. Cramer
Date
:
10 Sep 12 (Deposition) - 13 Feb 13 (Release) - 03 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.07
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (2x)
Keywords
:
Alpha Helix, Beta Sheet, Plastoquinol-Plastocyanin Oxidoreductase, Plastocyanin, Thylakoid Membrane, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. S. Hasan, E. Yamashita, D. Baniulis, W. A. Cramer
Quinone-Dependent Proton Transfer Pathways In The Photosynthetic Cytochrome B6F Complex
Proc. Natl. Acad. Sci. Usa V. 110 4297 2013
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Hetero Components
(13, 19)
Info
All Hetero Components
01a: (1R)-2-(DODECANOYLOXY)-1-[(PHOSPHO... (7PHa)
02a: OCTADECANE (8K6a)
03a: BETA-CAROTENE (BCRa)
04a: CADMIUM ION (CDa)
05a: CHLOROPHYLL A (CLAa)
06a: FE2/S2 (INORGANIC) CLUSTER (FESa)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
07c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
07d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
08a: PENTADECANE (MYSa)
09a: N-OCTANE (OCTa)
10a: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCa)
10b: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCb)
11a: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO... (SQDa)
12a: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2... (TDSa)
12b: 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2... (TDSb)
13a: UNDECYL-MALTOSIDE (UMQa)
13b: UNDECYL-MALTOSIDE (UMQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
7PH
1
Ligand/Ion
(1R)-2-(DODECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYLTETRADECANOATE
2
8K6
1
Ligand/Ion
OCTADECANE
3
BCR
1
Ligand/Ion
BETA-CAROTENE
4
CD
1
Ligand/Ion
CADMIUM ION
5
CLA
1
Ligand/Ion
CHLOROPHYLL A
6
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
7
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
MYS
1
Ligand/Ion
PENTADECANE
9
OCT
1
Ligand/Ion
N-OCTANE
10
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
11
SQD
1
Ligand/Ion
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
12
TDS
2
Ligand/Ion
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
13
UMQ
2
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
GLU A:75 , HOH A:401 , HIS C:143 , HOH C:401
BINDING SITE FOR RESIDUE CD A 301
02
AC2
SOFTWARE
PHE A:44 , GLN A:47 , GLY A:51 , PHE A:52 , MET A:54 , ARG A:83 , HIS A:86 , ARG A:87 , 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 302
03
AC3
SOFTWARE
TYR A:34 , GLY A:37 , GLY A:38 , THR A:40 , MET A:93 , MET A:97 , HIS A:100 , VAL A:101 , ARG A:103 , GLY A:109 , ARG A:114 , THR A:117 , TRP A:118 , GLY A:121 , VAL A:122 , HIS A:202 , PHE A:203 , ILE A:206 , ILE A:211 , SER A:212 , HEM A:304 , HOH A:402 , HOH A:403
BINDING SITE FOR RESIDUE HEM A 303
04
AC4
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , LEU A:41 , ILE A:206 , ARG A:207 , GLY A:210 , ILE A:211 , HEM A:303 , HOH A:402 , HOH A:407 , HOH A:408 , ASN B:25 , PHE B:40 , TDS B:201 , ARG H:26
BINDING SITE FOR RESIDUE HEM A 304
05
AC5
SOFTWARE
MET A:92 , CYS B:50 , PRO C:37 , GLN C:38 , TYR E:8 , GLU F:3 , GLU F:4 , TYR F:7 , ALA F:8 , LEU G:5 , LEU G:9 , BCR G:101 , VAL H:5 , TRP H:8 , LEU H:12 , PHE H:15
BINDING SITE FOR RESIDUE OPC A 305
06
AC6
SOFTWARE
LEU A:169
BINDING SITE FOR RESIDUE MYS A 306
07
AC7
SOFTWARE
VAL A:197
BINDING SITE FOR RESIDUE 8K6 A 307
08
AC8
SOFTWARE
ASN A:3 , GLN A:15 , UMQ B:202
BINDING SITE FOR RESIDUE UMQ A 308
09
AC9
SOFTWARE
TYR A:136 , ALA A:147 , ILE A:150 , LEU B:76 , PRO B:77 , LEU B:81 , PHE B:85 , LEU B:88 , CYS D:128 , HIS D:129
BINDING SITE FOR RESIDUE TDS A 309
10
BC1
SOFTWARE
LYS A:24 , ARG A:207 , HEM A:304 , ALA B:31 , ASP B:35 , LEU B:36 , LEU B:37 , PHE B:40 , PRO B:41
BINDING SITE FOR RESIDUE TDS B 201
11
BC2
SOFTWARE
THR A:22 , UMQ A:308 , TRP B:32 , SQD D:201
BINDING SITE FOR RESIDUE UMQ B 202
12
BC3
SOFTWARE
ILE A:98 , TYR A:105 , TYR B:80 , PRO B:83 , VAL B:84 , MET B:101 , LEU B:108 , ILE B:132 , PHE B:133 , GLY B:136 , THR B:140 , OPC B:204 , HOH B:301 , HOH B:303 , HOH B:304
BINDING SITE FOR RESIDUE CLA B 203
13
BC4
SOFTWARE
LEU B:100 , VAL B:111 , GLU B:115 , ASN B:118 , ARG B:126 , PRO B:127 , VAL B:128 , ALA B:129 , ILE B:132 , CLA B:203
BINDING SITE FOR RESIDUE OPC B 204
14
BC5
SOFTWARE
TRP C:257 , GLY D:33 , ALA D:34 , TYR D:36
BINDING SITE FOR RESIDUE 7PH C 301
15
BC6
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 , VAL C:75 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , ILE C:160 , TYR C:161
BINDING SITE FOR RESIDUE HEM C 302
16
BC7
SOFTWARE
TRP B:32 , PRO B:33 , TYR B:38 , UMQ B:202 , LYS C:275 , VAL C:279 , ARG D:16 , ASN D:20 , GLY D:25
BINDING SITE FOR RESIDUE SQD D 201
17
BC8
SOFTWARE
CYS D:108 , HIS D:110 , LEU D:111 , CYS D:126 , HIS D:129 , GLY D:130
BINDING SITE FOR RESIDUE FES D 202
18
BC9
SOFTWARE
ILE A:39 , MET A:96 , OPC A:305 , ILE F:16 , PHE F:17 , ALA G:16 , GLY G:19 , GLY G:20 , ILE H:19
BINDING SITE FOR RESIDUE BCR G 101
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
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[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(7, 7)
Info
All SCOP Domains
1a: SCOP_d4h13d2 (D:46-179)
2a: SCOP_d4h13b_ (B:)
3a: SCOP_d4h13a_ (A:)
4a: SCOP_d4h13d1 (D:9-45)
5a: SCOP_d4h13g_ (G:)
6a: SCOP_d4h13f_ (F:)
7a: SCOP_d4h13h_ (H:)
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Classes
(
)
(
)
Folds
(
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(
)
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(
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(
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(
)
(
)
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
d4h13d2
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
d4h13b_
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)
3a
d4h13a_
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
d4h13d1
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
d4h13g_
G:
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)
6a
d4h13f_
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)
7a
d4h13h_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Asym.Unit (347 KB)
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