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1KBY
Biol. Unit 1
Info
Asym.Unit (157 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER WITH BACTERIOCHLOROPHYLL-BACTERIOPHEOPHYTIN HETERODIMER
Authors
:
A. Camara-Artigas, C. Magee, A. Goetsch, J. P. Allen
Date
:
07 Nov 01 (Deposition) - 13 Nov 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Transmembrane Alpha Helix, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Camara-Artigas, C. Magee, A. Goetsch, J. P. Allen
The Structure Of The Heterodimer Reaction Center From Rhodobacter Sphaeroides At 2. 55 A Resolution.
Photosynth. Res. V. 74 87 2002
(for further references see the
PDB file header
)
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Hetero Components
(5, 9)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
2c: BACTERIOPHEOPHYTIN A (BPHc)
3a: CARDIOLIPIN (CDLa)
4a: CHLORIDE ION (CLa)
5a: FE (III) ION (FEa)
6a: SPHEROIDENE (SPOa)
7a: UBIQUINONE-10 (U10a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
3
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
3
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CDL
1
Ligand/Ion
CARDIOLIPIN
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
FE
-1
Ligand/Ion
FE (III) ION
6
SPO
1
Ligand/Ion
SPHEROIDENE
7
U10
1
Ligand/Ion
UBIQUINONE-10
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M 856
02
AC2
SOFTWARE
LYS L:82
BINDING SITE FOR RESIDUE CL M 6000
03
AC3
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:851 , BPH L:854 , HOH L:1008 , TRP M:157 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BPH M:852 , SPO M:859
BINDING SITE FOR RESIDUE BCL L 850
04
AC4
SOFTWARE
PHE L:97 , ALA L:124 , ALA L:127 , LEU L:131 , VAL L:157 , PHE L:167 , HIS L:168 , HIS L:173 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:850 , BCL L:853 , BPH M:852
BINDING SITE FOR RESIDUE BCL L 851
05
AC5
SOFTWARE
VAL L:157 , TYR L:162 , PHE L:181 , BCL L:850 , BCL L:851 , BCL L:853 , BPH L:854 , ALA M:153 , THR M:186 , ASN M:187 , LEU M:196 , PHE M:197 , LEU M:202 , SER M:205 , ILE M:206 , TYR M:210 , THR M:277 , GLY M:280 , ILE M:284
BINDING SITE FOR RESIDUE BPH M 852
06
AC6
SOFTWARE
ILE L:49 , TYR L:128 , LEU L:131 , PHE L:146 , HIS L:153 , LEU L:154 , BCL L:851 , BPH L:855 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , BPH M:852
BINDING SITE FOR RESIDUE BCL L 853
07
AC7
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , BCL L:850 , LEU M:64 , PHE M:67 , ALA M:125 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:273 , THR M:277 , BPH M:852
BINDING SITE FOR RESIDUE BPH L 854
08
AC8
SOFTWARE
ILE L:46 , TRP L:100 , GLU L:104 , ALA L:120 , PHE L:121 , TYR L:148 , LEU L:238 , VAL L:241 , BCL L:853 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH L 855
09
AC9
SOFTWARE
THR L:38 , TRP L:100 , MET M:218 , HIS M:219 , THR M:222 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , MET M:262 , ILE M:265 , MET M:272
BINDING SITE FOR RESIDUE U10 M 857
10
BC1
SOFTWARE
BCL L:850 , PHE M:67 , ILE M:70 , GLY M:71 , TRP M:75 , PHE M:120 , TRP M:157 , LEU M:160 , PHE M:162 , TRP M:171 , TYR M:177 , GLY M:178 , HIS M:182
BINDING SITE FOR RESIDUE SPO M 859
11
BC2
SOFTWARE
TYR H:30 , ASN L:199 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , TRP M:155 , ARG M:267 , TRP M:271 , HOH M:1198
BINDING SITE FOR RESIDUE CDL M 5000
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (M:195-221)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOS4
167-193
1
L:166-192
RCEL_RHOSH
167-193
1
L:166-192
RCEM_RHOS4
196-222
1
M:195-221
RCEM_RHOSH
196-222
1
M:195-221
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1kbyh1 (H:36-246)
2a: SCOP_d1kbyl_ (L:)
3a: SCOP_d1kbym_ (M:)
4a: SCOP_d1kbyh2 (H:11-35)
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)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d1kbyh1
H:36-246
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)
2a
d1kbyl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1kbym_
M:
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)
4a
d1kbyh2
H:11-35
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1kbyH02 (H:117-246)
2a: CATH_1kbyH01 (H:12-116)
3a: CATH_1kbyM01 (M:1-143)
3b: CATH_1kbyM02 (M:144-302)
3c: CATH_1kbyL01 (L:1-163)
3d: CATH_1kbyL02 (L:164-263)
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)
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)
(
)
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.
(10)
1a
1kbyH02
H:117-246
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.
(10)
2a
1kbyH01
H:12-116
Class
:
Mainly Alpha
(13335)
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.
(10)
3a
1kbyM01
M:1-143
3b
1kbyM02
M:144-302
3c
1kbyL01
L:1-163
3d
1kbyL02
L:164-263
[
close CATH info
]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_1kbyH01 (H:141-212)
2a: PFAM_PRCH_1kbyH02 (H:11-137)
3a: PFAM_Photo_RC_1kbyL01 (L:29-272)
3b: PFAM_Photo_RC_1kbyM01 (M:50-302)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1kbyH01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1kbyH02
H:11-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1kbyL01
L:29-272
3b
Photo_RC-1kbyM01
M:50-302
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]
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Asymmetric Unit 1
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