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1DS8
Biol. Unit 1
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: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
13: BC7 (SOFTWARE)
14: BC8 (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 FE2 M 1007
02
AC2
SOFTWARE
ASP H:124 , HIS H:126 , HIS H:128 , HOH H:1043 , HOH H:1048 , HOH H:1086
BINDING SITE FOR RESIDUE CD H 1010
03
AC3
SOFTWARE
HOH L:1023 , HIS M:145 , ARG M:267 , LDA M:1012
BINDING SITE FOR RESIDUE CL M 1011
04
AC7
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , LEU L:185 , BCL L:1002 , HOH L:1013 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1003 , BPH M:1005 , LDA M:1014
BINDING SITE FOR RESIDUE BCL L 1001
05
AC8
SOFTWARE
PHE L:97 , ALA L:127 , LEU L:131 , VAL L:157 , TYR L:162 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ILE L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:1001 , BCL L:1004 , BPH L:1006 , TYR M:210 , BCL M:1003
BINDING SITE FOR RESIDUE BCL L 1002
06
AC9
SOFTWARE
VAL L:157 , PHE L:181 , BCL L:1001 , BCL L:1002 , BCL L:1004 , ALA M:153 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , GLY M:280 , ILE M:284 , BPH M:1005
BINDING SITE FOR RESIDUE BCL M 1003
07
BC1
SOFTWARE
LEU L:131 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:1002 , BPH L:1006 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , GLY M:211 , LEU M:214 , BCL M:1003 , U10 M:1008 , LDA M:1013 , HOH M:1016
BINDING SITE FOR RESIDUE BCL L 1004
08
BC2
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , BCL L:1001 , U10 L:1009 , SER M:59 , GLY M:63 , ALA M:125 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:1003
BINDING SITE FOR RESIDUE BPH M 1005
09
BC3
SOFTWARE
PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , PHE L:123 , ALA L:124 , TYR L:148 , HIS L:153 , VAL L:241 , BCL L:1002 , BCL L:1004 , TYR M:210 , ALA M:213 , LEU M:214 , MET M:218 , TRP M:252
BINDING SITE FOR RESIDUE BPH L 1006
10
BC4
SOFTWARE
BCL L:1004 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , THR M:261 , MET M:262 , ILE M:265 , TRP M:268
BINDING SITE FOR RESIDUE U10 M 1008
11
BC5
SOFTWARE
LEU L:189 , LEU L:193 , PHE L:216 , VAL L:220 , GLY L:221 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229 , HOH L:1070 , SER M:30 , GLY M:31 , GLY M:33 , BPH M:1005
BINDING SITE FOR RESIDUE U10 L 1009
12
BC6
SOFTWARE
HIS M:145 , TRP M:148 , ILE M:270 , LEU M:278 , CL M:1011
BINDING SITE FOR RESIDUE LDA M 1012
13
BC7
SOFTWARE
BCL L:1004 , PRO M:200 , PHE M:208
BINDING SITE FOR RESIDUE LDA M 1013
14
BC8
SOFTWARE
BCL L:1001 , TRP M:115 , MET M:122 , GLY M:161 , ALA M:174 , VAL M:175 , TYR M:177
BINDING SITE FOR RESIDUE LDA M 1014
[
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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:
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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
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
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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)
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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
[
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]
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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)
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)
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(
)
(
)
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)
Header - Asym.Unit
Biol.Unit 1 (151 KB)
Header - Biol.Unit 1
Biol.Unit 2 (147 KB)
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