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1DS8
Biol. Unit 2
Info
Asym.Unit (305 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (147 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR CD2+
Authors
:
H. L. Axelrod, E. C. Abresch, M. L. Paddock, M. Y. Okamura, G. Feher
Date
:
07 Jan 00 (Deposition) - 08 Mar 00 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : H,L,M,R,S,T
Biol. Unit 1: H,L,M (1x)
Biol. Unit 2: R,S,T (1x)
Keywords
:
Bacterial Photosynthesis, Rhodobacter Sphaeroides, Metal Ion Binding, Cation Binding, Proton Transfer, Integral Membrane Protein, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Axelrod, E. C. Abresch, M. L. Paddock, M. Y. Okamura, G. Feher
Determination Of The Binding Sites Of The Proton Transfer Inhibitors Cd2+ And Zn2+ In Bacterial Reaction Centers.
Proc. Natl. Acad. Sci. Usa V. 97 1542 2000
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 12)
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: CADMIUM ION (CDa)
3b: CADMIUM ION (CDb)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
5a: FE (II) ION (FE2a)
5b: FE (II) ION (FE2b)
6a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
6b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
6c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
6d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
6e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
6f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
7a: UBIQUINONE-10 (U10a)
7b: UBIQUINONE-10 (U10b)
7c: UBIQUINONE-10 (U10c)
7d: UBIQUINONE-10 (U10d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CD
-1
Ligand/Ion
CADMIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
FE2
1
Ligand/Ion
FE (II) ION
6
LDA
3
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
2
Ligand/Ion
UBIQUINONE-10
[
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]
Sites
(14, 14)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
HIS R:190 , HIS R:230 , HIS S:219 , GLU S:234 , HIS S:266
BINDING SITE FOR RESIDUE FE2 S 2007
02
AC5
SOFTWARE
ASP T:124 , HIS T:126 , HIS T:128 , HOH T:2027 , HOH T:2066 , HOH T:2095
BINDING SITE FOR RESIDUE CD T 2010
03
AC6
SOFTWARE
HOH R:2015 , HIS S:145 , ARG S:267 , LDA S:2013
BINDING SITE FOR RESIDUE CL S 2011
04
BC9
SOFTWARE
HIS R:168 , MET R:174 , ILE R:177 , SER R:178 , THR R:182 , LEU R:185 , BCL R:2002 , HOH R:2056 , ILE S:179 , HIS S:182 , LEU S:183 , THR S:186 , BCL S:2003 , BPH S:2005 , LDA S:2012
BINDING SITE FOR RESIDUE BCL R 2001
05
CC1
SOFTWARE
PHE R:97 , LEU R:131 , VAL R:157 , TYR R:162 , ASN R:166 , PHE R:167 , HIS R:168 , HIS R:173 , ILE R:177 , PHE R:180 , SER R:244 , CYS R:247 , MET R:248 , BCL R:2001 , BCL R:2004 , BPH R:2006 , TYR S:210 , BCL S:2003
BINDING SITE FOR RESIDUE BCL R 2002
06
CC2
SOFTWARE
VAL R:157 , PHE R:181 , BCL R:2001 , BCL R:2002 , BCL R:2004 , ALA S:153 , LEU S:156 , THR S:186 , ASN S:187 , PHE S:189 , SER S:190 , LEU S:196 , PHE S:197 , HIS S:202 , SER S:205 , ILE S:206 , TYR S:210 , VAL S:276 , GLY S:280 , ILE S:284 , BPH S:2005
BINDING SITE FOR RESIDUE BCL S 2003
07
CC3
SOFTWARE
LEU R:131 , PHE R:146 , HIS R:153 , LEU R:154 , BCL R:2002 , BPH R:2006 , HOH R:2023 , HOH R:2059 , PHE S:197 , GLY S:203 , ILE S:206 , ALA S:207 , TYR S:210 , LEU S:214 , BCL S:2003 , U10 S:2008 , LDA S:2014
BINDING SITE FOR RESIDUE BCL R 2004
08
CC4
SOFTWARE
PHE R:181 , ALA R:184 , LEU R:185 , LEU R:189 , BCL R:2001 , SER S:59 , GLY S:63 , TRP S:129 , THR S:146 , ALA S:149 , PHE S:150 , ALA S:153 , ALA S:273 , BCL S:2003
BINDING SITE FOR RESIDUE BPH S 2005
09
CC5
SOFTWARE
ALA R:42 , GLY R:45 , ILE R:46 , PHE R:97 , TRP R:100 , GLU R:104 , ILE R:117 , ALA R:120 , PHE R:121 , TYR R:148 , GLY R:149 , ILE R:150 , HIS R:153 , LEU R:238 , VAL R:241 , BCL R:2002 , BCL R:2004 , HOH R:2059 , TYR S:210 , ALA S:213 , LEU S:214 , MET S:218 , TRP S:252 , MET S:256
BINDING SITE FOR RESIDUE BPH R 2006
10
CC6
SOFTWARE
BCL R:2004 , HIS S:219 , THR S:222 , ALA S:248 , ALA S:249 , TRP S:252 , MET S:256 , ASN S:259 , ALA S:260 , THR S:261 , ILE S:265 , TRP S:268
BINDING SITE FOR RESIDUE U10 S 2008
11
CC7
SOFTWARE
THR R:182 , LEU R:189 , PHE R:216 , TYR R:222 , SER R:223 , ILE R:224 , GLY R:225 , ILE R:229 , LEU R:232 , HOH R:2039
BINDING SITE FOR RESIDUE U10 R 2009
12
CC8
SOFTWARE
BCL R:2001 , PHE S:67 , ILE S:70 , GLY S:71 , PHE S:74 , PHE S:85 , TYR S:177 , GLY S:178
BINDING SITE FOR RESIDUE LDA S 2012
13
CC9
SOFTWARE
HIS S:145 , TRP S:148 , SER S:152 , TRP S:271 , LEU S:278 , CL S:2011
BINDING SITE FOR RESIDUE LDA S 2013
14
DC1
SOFTWARE
BCL R:2004 , PRO S:200 , TRP T:21
BINDING SITE FOR RESIDUE LDA S 2014
[
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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 (S:195-221)
;
View:
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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
-
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
[
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]
Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1ds8h1 (H:36-256)
1b: SCOP_d1ds8t1 (T:36-256)
2a: SCOP_d1ds8l_ (L:)
2b: SCOP_d1ds8r_ (R:)
3a: SCOP_d1ds8m_ (M:)
3b: SCOP_d1ds8s_ (S:)
4a: SCOP_d1ds8h2 (H:11-35)
4b: SCOP_d1ds8t2 (T:11-35)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1ds8h1
H:36-256
1b
d1ds8t1
T:36-256
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
d1ds8l_
L:
2b
d1ds8r_
R:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1ds8m_
M:
3b
d1ds8s_
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)
4a
d1ds8h2
H:11-35
4b
d1ds8t2
T:11-35
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1ds8H02 (H:117-249)
1b: CATH_1ds8T02 (T:117-249)
2a: CATH_1ds8H01 (H:12-116)
2b: CATH_1ds8T01 (T:12-116)
3a: CATH_1ds8M01 (M:3-143)
3b: CATH_1ds8M02 (M:144-301)
3c: CATH_1ds8S02 (S:144-301)
3d: CATH_1ds8L01 (L:1-163)
3e: CATH_1ds8R01 (R:1-163)
3f: CATH_1ds8L02 (L:164-263)
3g: CATH_1ds8R02 (R:164-263)
3h: CATH_1ds8S01 (S:3-143)
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Classes
(
)
(
)
Architectures
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)
(
)
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. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
1a
1ds8H02
H:117-249
1b
1ds8T02
T:117-249
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. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
2a
1ds8H01
H:12-116
2b
1ds8T01
T: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. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
3a
1ds8M01
M:3-143
3b
1ds8M02
M:144-301
3c
1ds8S02
S:144-301
3d
1ds8L01
L:1-163
3e
1ds8R01
R:1-163
3f
1ds8L02
L:164-263
3g
1ds8R02
R:164-263
3h
1ds8S01
S:3-143
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (305 KB)
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