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1VRN
Asym. Unit
Info
Asym.Unit (231 KB)
Biol.Unit 1 (218 KB)
Biol.Unit 2 (429 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER BLASTOCHLORIS VIRIDIS (ATCC)
Authors
:
R. H. G. Baxter, B. -L. Seagle, J. R. Norris
Date
:
23 Feb 05 (Deposition) - 22 Mar 05 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Biol. Unit 2: C,H,L,M (2x)
Keywords
:
Integral Membrane Protein; Ubiquinone; Secondary Quinone (Qb), Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. H. Baxter, B. L. Seagle, N. Ponomarenko, J. R. Norris
Cryogenic Structure Of The Photosynthetic Reaction Center O Blastochloris Viridis In The Light And Dark.
Acta Crystallogr. , Sect. D V. 61 605 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(10, 28)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL B (BCBa)
01b: BACTERIOCHLOROPHYLL B (BCBb)
01c: BACTERIOCHLOROPHYLL B (BCBc)
01d: BACTERIOCHLOROPHYLL B (BCBd)
02a: BACTERIOPHEOPHYTIN B (BPBa)
02b: BACTERIOPHEOPHYTIN B (BPBb)
03a: FE (II) ION (FE2a)
04a: N-FORMYLMETHIONINE (FMEa)
05a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
05b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
05c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
05d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
06a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
06b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
06c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
06d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
06e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
06f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
07a: MENAQUINONE-9 (MQ9a)
08a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
09a: SULFATE ION (SO4a)
09b: SULFATE ION (SO4b)
09c: SULFATE ION (SO4c)
09d: SULFATE ION (SO4d)
09e: SULFATE ION (SO4e)
09f: SULFATE ION (SO4f)
09g: SULFATE ION (SO4g)
10a: UBIQUINONE-7 (UQ7a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCB
4
Ligand/Ion
BACTERIOCHLOROPHYLL B
2
BPB
2
Ligand/Ion
BACTERIOPHEOPHYTIN B
3
FE2
1
Ligand/Ion
FE (II) ION
4
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
5
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
LDA
6
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
MQ9
1
Ligand/Ion
MENAQUINONE-9
8
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
9
SO4
7
Ligand/Ion
SULFATE ION
10
UQ7
1
Ligand/Ion
UBIQUINONE-7
[
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]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264
BINDING SITE FOR RESIDUE FE2 M 500
02
AC2
SOFTWARE
HOH H:1437 , ASN L:199 , HOH L:1289 , HOH L:1290 , HIS M:143 , ARG M:265
BINDING SITE FOR RESIDUE SO4 M 801
03
AC3
SOFTWARE
ARG H:33 , ARG H:37 , TYR H:41 , GLU H:61 , HOH H:1397 , HOH H:1514 , HOH H:1531 , ARG M:251
BINDING SITE FOR RESIDUE SO4 H 802
04
AC4
SOFTWARE
LEU H:246 , HOH H:1498 , ALA M:1 , ARG M:226 , HOH M:1323 , HOH M:1324
BINDING SITE FOR RESIDUE SO4 M 803
05
AC5
SOFTWARE
TRP M:23 , TYR M:50 , ALA M:53 , SER M:54 , SER M:133 , LDA M:704 , HOH M:1347 , HOH M:1353
BINDING SITE FOR RESIDUE SO4 M 804
06
AC6
SOFTWARE
SER M:35 , TYR M:36 , TRP M:37
BINDING SITE FOR RESIDUE SO4 M 805
07
AC7
SOFTWARE
TYR H:117 , GLU H:119 , ARG H:233 , LYS H:237
BINDING SITE FOR RESIDUE SO4 H 806
08
AC8
SOFTWARE
LEU H:30 , ARG H:34 , LDA H:703
BINDING SITE FOR RESIDUE SO4 H 807
09
AC9
SOFTWARE
TYR C:56 , LYS C:57 , ASN C:58 , VAL C:59 , LYS C:60 , VAL C:61 , LEU C:62 , PHE C:70 , MET C:74 , THR C:78 , SER C:82 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , TYR C:104 , ALA C:107 , ARG C:108 , VAL C:212
BINDING SITE FOR RESIDUE HEM C 401
10
BC1
SOFTWARE
ILE C:77 , TYR C:89 , TYR C:102 , PRO C:103 , VAL C:106 , MET C:110 , LEU C:111 , MET C:113 , THR C:114 , THR C:131 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , ARG C:293 , PRO C:301
BINDING SITE FOR RESIDUE HEM C 402
11
BC2
SOFTWARE
VAL C:201 , ARG C:202 , VAL C:203 , VAL C:204 , MET C:233 , SER C:237 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , PHE C:253 , GLU C:254 , ARG C:264 , ALA C:267 , TRP C:268 , ILE C:271 , ARG C:272 , HOH C:1139 , HOH C:1142 , HOH C:1166 , HOH C:1177 , TYR L:162 , ILE M:189
BINDING SITE FOR RESIDUE HEM C 403
12
BC3
SOFTWARE
HIS C:124 , VAL C:125 , THR C:128 , GLY C:129 , ILE C:236 , LEU C:240 , PHE C:246 , GLN C:263 , ILE C:266 , MET C:273 , ASP C:304 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315 , HOH C:1143 , HOH C:1189
BINDING SITE FOR RESIDUE HEM C 404
13
BC4
SOFTWARE
MET L:174 , VAL L:177 , SER L:178 , PHE L:181 , VAL L:182 , MET L:185 , VAL L:220 , BCB L:402 , UQ7 L:502 , PHE M:154 , VAL M:155 , ILE M:177 , HIS M:180 , ILE M:181 , LEU M:184 , BCB M:403 , BPB M:405 , NS5 M:600 , HOH M:1285
BINDING SITE FOR RESIDUE BCB M 401
14
BC5
SOFTWARE
PRO L:124 , MET L:127 , PHE L:128 , VAL L:157 , ASN L:158 , PHE L:160 , TYR L:162 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , VAL L:177 , PHE L:181 , ILE L:240 , PHE L:241 , GLY L:244 , THR L:248 , BCB L:404 , BPB L:406 , TYR M:195 , TYR M:208 , BCB M:401 , BCB M:403
BINDING SITE FOR RESIDUE BCB L 402
15
BC6
SOFTWARE
TYR L:162 , PHE L:181 , BCB L:402 , BCB L:404 , ILE M:69 , PHE M:148 , PHE M:154 , VAL M:155 , LEU M:184 , SER M:188 , PHE M:194 , TYR M:195 , HIS M:200 , SER M:203 , ILE M:204 , TYR M:208 , MET M:275 , ALA M:278 , ILE M:282 , BCB M:401 , BPB M:405
BINDING SITE FOR RESIDUE BCB M 403
16
BC7
SOFTWARE
ILE L:49 , PHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , VAL L:157 , BCB L:402 , BPB L:406 , LDA L:706 , HOH L:1377 , TYR M:195 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , PHE M:270 , BCB M:403 , MQ9 M:501
BINDING SITE FOR RESIDUE BCB L 404
17
BC8
SOFTWARE
PHE L:181 , MET L:185 , LEU L:189 , PHE M:59 , ILE M:66 , SER M:123 , LEU M:124 , TRP M:127 , VAL M:131 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271 , BCB M:401 , BCB M:403
BINDING SITE FOR RESIDUE BPB M 405
18
BC9
SOFTWARE
PHE L:41 , ILE L:42 , ILE L:49 , PHE L:97 , TRP L:100 , GLU L:104 , VAL L:117 , PHE L:121 , PRO L:124 , TYR L:148 , GLY L:149 , ILE L:150 , HIS L:153 , ALA L:237 , PHE L:241 , BCB L:402 , BCB L:404 , TYR M:208 , LEU M:212 , TRP M:250 , ILE M:254 , MQ9 M:501
BINDING SITE FOR RESIDUE BPB L 406
19
CC1
SOFTWARE
LDA H:701 , TYR L:29 , PHE L:43 , ARG L:103 , BCB L:404 , BPB L:406 , HIS M:217 , THR M:220 , ALA M:246 , TRP M:250 , ILE M:254 , PHE M:256 , ASN M:257 , ALA M:258 , THR M:259 , ILE M:260 , VAL M:263 , TRP M:266
BINDING SITE FOR RESIDUE MQ9 M 501
20
CC2
SOFTWARE
SER L:175 , SER L:178 , PHE L:179 , VAL L:182 , HIS L:190 , LEU L:193 , ILE L:194 , GLU L:212 , ASN L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , ALA L:226 , ILE L:229 , LEU L:232 , PHE L:246 , BCB M:401
BINDING SITE FOR RESIDUE UQ7 L 502
21
CC3
SOFTWARE
LEU M:70 , PHE M:88 , LEU M:114 , GLY M:117 , MET M:120 , THR M:121 , GLY M:159 , TRP M:169 , VAL M:173 , GLY M:176 , HIS M:180 , BCB M:401
BINDING SITE FOR RESIDUE NS5 M 600
22
CC4
SOFTWARE
ARG H:33 , ASP H:56 , PHE M:256 , PHE M:270 , MQ9 M:501
BINDING SITE FOR RESIDUE LDA H 701
23
CC5
SOFTWARE
TRP H:17 , ASP L:60 , TYR M:195 , PRO M:198 , TRP M:295 , HIS M:299
BINDING SITE FOR RESIDUE LDA L 702
24
CC6
SOFTWARE
LEU H:30 , VAL H:59 , TYR H:60 , LEU H:62 , TYR H:64 , ARG H:80 , ARG H:81 , SO4 H:807 , HOH H:1461
BINDING SITE FOR RESIDUE LDA H 703
25
CC7
SOFTWARE
TRP M:23 , SER M:54 , SER M:126 , SO4 M:804
BINDING SITE FOR RESIDUE LDA M 704
26
CC8
SOFTWARE
PHE M:71 , ASN M:72 , TRP M:112
BINDING SITE FOR RESIDUE LDA M 705
27
CC9
SOFTWARE
TYR L:29 , BCB L:404 , ILE M:254
BINDING SITE FOR RESIDUE LDA L 706
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (C:82-314)
2: REACTION_CENTER (L:166-192,M:193-219)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
CYCR_BLAVI
102-334
1
C:82-314
2
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_BLAVI
167-193
1
L:166-192
RCEM_BLAVI
194-220
1
M:193-219
[
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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, 5)
Info
All SCOP Domains
1a: SCOP_d1vrnc_ (C:)
2a: SCOP_d1vrnh2 (H:37-258)
3a: SCOP_d1vrnl_ (L:)
3b: SCOP_d1vrnm_ (M:)
4a: SCOP_d1vrnh1 (H:1-36)
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(
)
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(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Photosynthetic reaction centre (cytochrome subunit)
(20)
Protein domain
:
Photosynthetic reaction centre (cytochrome subunit)
(19)
Rhodopseudomonas viridis [TaxId: 1079]
(18)
1a
d1vrnc_
C:
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)
Rhodopseudomonas viridis [TaxId: 1079]
(15)
2a
d1vrnh2
H:37-258
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
:
automated matches
(44)
Blastochloris viridis [TaxId: 1079]
(7)
3a
d1vrnl_
L:
3b
d1vrnm_
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)
Rhodopseudomonas viridis [TaxId: 1079]
(15)
4a
d1vrnh1
H:1-36
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1vrnH02 (H:120-258)
2a: CATH_1vrnH01 (H:2-119)
3a: CATH_1vrnC02 (C:143-205,C:221-313)
3b: CATH_1vrnC01 (C:24-142,C:314-332)
4a: CATH_1vrnM01 (M:1-143)
4b: CATH_1vrnM02 (M:144-302)
4c: CATH_1vrnL01 (L:1-165)
4d: CATH_1vrnL02 (L:166-273)
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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)
Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079.
(3)
1a
1vrnH02
H:120-258
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)
Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079.
(3)
2a
1vrnH01
H:2-119
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Photosynthetic Reaction Center, subunit C; domain 2
(18)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit C, domain 2
(18)
Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079.
(3)
3a
1vrnC02
C:143-205,C:221-313
3b
1vrnC01
C:24-142,C:314-332
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079. Blastochloris viridis. Organism_taxid: 1079.
(3)
4a
1vrnM01
M:1-143
4b
1vrnM02
M:144-302
4c
1vrnL01
L:1-165
4d
1vrnL02
L:166-273
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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