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1DS8
Asym. Unit
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
(7, 28)
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
8
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
4
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CD
2
Ligand/Ion
CADMIUM ION
4
CL
2
Ligand/Ion
CHLORIDE ION
5
FE2
2
Ligand/Ion
FE (II) ION
6
LDA
6
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
4
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(28, 28)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (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
AC4
SOFTWARE
HIS R:190 , HIS R:230 , HIS S:219 , GLU S:234 , HIS S:266
BINDING SITE FOR RESIDUE FE2 S 2007
05
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
06
AC6
SOFTWARE
HOH R:2015 , HIS S:145 , ARG S:267 , LDA S:2013
BINDING SITE FOR RESIDUE CL S 2011
07
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
08
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
09
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
10
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
11
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
12
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
13
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
14
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
15
BC6
SOFTWARE
HIS M:145 , TRP M:148 , ILE M:270 , LEU M:278 , CL M:1011
BINDING SITE FOR RESIDUE LDA M 1012
16
BC7
SOFTWARE
BCL L:1004 , PRO M:200 , PHE M:208
BINDING SITE FOR RESIDUE LDA M 1013
17
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
18
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
19
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
20
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
21
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
22
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
23
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
24
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
25
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
26
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
27
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
28
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 not available)
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 (L:166-192,R:166-192,L:166-192,R:16...)
;
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
2
L:166-192
R:166-192
RCEL_RHOSH
167-193
2
L:166-192
R:166-192
RCEM_RHOS4
196-222
2
M:195-221
S:195-221
RCEM_RHOSH
196-222
2
M:195-221
S:195-221
[
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]
Exons
(0, 0)
Info
All Exons
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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
(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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Superfamilies
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Families
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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
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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)
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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