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1DV3
Biol. Unit 2
Info
Asym.Unit (300 KB)
Biol.Unit 1 (149 KB)
Biol.Unit 2 (146 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+
Authors
:
H. L. Axelrod, E. C. Abresch, M. L. Paddock, M. Y. Okamura, G. Feher
Date
:
19 Jan 00 (Deposition) - 08 Mar 00 (Release) - 13 Jul 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
(4, 9)
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)
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
-1
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
U10
2
Ligand/Ion
UBIQUINONE-10
[
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]
Sites
(11, 11)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC6 (SOFTWARE)
04: BC8 (SOFTWARE)
05: BC9 (SOFTWARE)
06: CC1 (SOFTWARE)
07: CC2 (SOFTWARE)
08: CC3 (SOFTWARE)
09: CC4 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC6 (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:2023 , HOH T:2024
BINDING SITE FOR RESIDUE CD T 2010
03
AC6
SOFTWARE
HIS S:145 , ARG S:267
BINDING SITE FOR RESIDUE CL S 2011
04
BC8
SOFTWARE
HIS R:168 , MET R:174 , ILE R:177 , SER R:178 , THR R:182 , HOH R:2023 , ILE S:179 , HIS S:182 , LEU S:183 , THR S:186 , BCL S:2003 , BPH S:2005
BINDING SITE FOR RESIDUE BCL S 2001
05
BC9
SOFTWARE
PHE R:97 , LEU R:131 , VAL R:157 , 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:2004 , BPH R:2006 , TYR S:210 , BCL S:2003
BINDING SITE FOR RESIDUE BCL R 2002
06
CC1
SOFTWARE
VAL R:157 , PHE R:181 , BCL R:2002 , BCL R:2004 , ALA S:153 , LEU S:156 , THR S:186 , ASN S:187 , SER S:190 , LEU S:196 , PHE S:197 , HIS S:202 , SER S:205 , ILE S:206 , TYR S:210 , GLY S:280 , ILE S:284 , BCL S:2001 , BPH S:2005
BINDING SITE FOR RESIDUE BCL S 2003
07
CC2
SOFTWARE
LEU R:131 , HIS R:153 , LEU R:154 , BCL R:2002 , BPH R:2006 , HOH R:2028 , PHE S:197 , GLY S:203 , ILE S:206 , ALA S:207 , TYR S:210 , LEU S:214 , BCL S:2003
BINDING SITE FOR RESIDUE BCL R 2004
08
CC3
SOFTWARE
PHE R:181 , ALA R:184 , LEU R:185 , LEU R:189 , SER S:59 , GLY S:63 , TRP S:129 , THR S:146 , PHE S:150 , ALA S:153 , ALA S:273 , BCL S:2001 , BCL S:2003
BINDING SITE FOR RESIDUE BPH S 2005
09
CC4
SOFTWARE
ALA R:42 , GLY R:45 , PHE R:97 , TRP R:100 , GLU R:104 , ILE R:117 , ALA R:120 , PHE R:121 , TYR R:148 , HIS R:153 , LEU R:238 , VAL R:241 , BCL R:2002 , BCL R:2004 , TYR S:210 , ALA S:213 , LEU S:214 , TRP S:252 , MET S:256
BINDING SITE FOR RESIDUE BPH R 2006
10
CC5
SOFTWARE
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
CC6
SOFTWARE
LEU R:189 , HIS R:190 , LEU R:193 , GLU R:212 , ASP R:213 , PHE R:216 , TYR R:222 , SER R:223 , ILE R:224 , GLY R:225 , THR R:226 , ILE R:229
BINDING SITE FOR RESIDUE U10 R 2009
[
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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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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_d1dv3h1 (H:36-256)
1b: SCOP_d1dv3t1 (T:36-256)
2a: SCOP_d1dv3l_ (L:)
2b: SCOP_d1dv3r_ (R:)
3a: SCOP_d1dv3m_ (M:)
3b: SCOP_d1dv3s_ (S:)
4a: SCOP_d1dv3h2 (H:11-35)
4b: SCOP_d1dv3t2 (T:11-35)
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)
(
)
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(
)
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)
(
)
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
d1dv3h1
H:36-256
1b
d1dv3t1
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
d1dv3l_
L:
2b
d1dv3r_
R:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1dv3m_
M:
3b
d1dv3s_
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
d1dv3h2
H:11-35
4b
d1dv3t2
T:11-35
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1dv3H02 (H:117-249)
1b: CATH_1dv3T02 (T:117-249)
2a: CATH_1dv3H01 (H:12-116)
2b: CATH_1dv3T01 (T:12-116)
3a: CATH_1dv3M01 (M:3-143)
3b: CATH_1dv3S01 (S:3-143)
3c: CATH_1dv3M02 (M:144-301)
3d: CATH_1dv3S02 (S:144-301)
3e: CATH_1dv3L01 (L:1-163)
3f: CATH_1dv3R01 (R:1-163)
3g: CATH_1dv3L02 (L:164-263)
3h: CATH_1dv3R02 (R: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. Rhodobacter sphaeroides. Organism_taxid: 1063.
(21)
1a
1dv3H02
H:117-249
1b
1dv3T02
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
1dv3H01
H:12-116
2b
1dv3T01
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
1dv3M01
M:3-143
3b
1dv3S01
S:3-143
3c
1dv3M02
M:144-301
3d
1dv3S02
S:144-301
3e
1dv3L01
L:1-163
3f
1dv3R01
R:1-163
3g
1dv3L02
L:164-263
3h
1dv3R02
R:164-263
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (300 KB)
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