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6PRC
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (216 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (DG-420314 (TRIAZINE) COMPLEX)
Authors
:
C. R. D. Lancaster, H. Michel
Date
:
31 Jul 97 (Deposition) - 06 Apr 99 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Photosynthetic Reaction Center, Secondary Quinone (Qb)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. R. Lancaster, H. Michel
Refined Crystal Structures Of Reaction Centres From Rhodopseudomonas Viridis In Complexes With The Herbicide Atrazine And Two Chiral Atrazine Derivatives Also Lead To A New Model Of The Bound Carotenoid.
J. Mol. Biol. V. 286 883 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(10, 25)
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: 2-CHLORO-4-ETHYLAMINO-6-(S(-)-2'-C... (CEBa)
04a: FE (II) ION (FE2a)
05a: N-FORMYLMETHIONINE (FMEa)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
06b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
06c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
06d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
07c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
07d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
07e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
07f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
08a: MENAQUINONE-7 (MQ7a)
09a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
10d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCB
4
Ligand/Ion
BACTERIOCHLOROPHYLL B
2
BPB
2
Ligand/Ion
BACTERIOPHEOPHYTIN B
3
CEB
1
Ligand/Ion
2-CHLORO-4-ETHYLAMINO-6-(S(-)-2'-CYANO-4-BUTYLAMINO)-1,3,5-TRIAZINE
4
FE2
1
Ligand/Ion
FE (II) ION
5
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
LDA
6
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
MQ7
1
Ligand/Ion
MENAQUINONE-7
9
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
10
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(24, 24)
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)
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
ARG H:33 , ARG H:37 , TYR H:41 , LEU H:43 , HOH H:1061 , HOH H:1181 , ARG M:251 , HOH M:1062
BINDING SITE FOR RESIDUE SO4 H 801
03
AC3
SOFTWARE
HOH H:1231 , ASN L:199 , HIS M:143 , ARG M:265 , HOH M:1130
BINDING SITE FOR RESIDUE SO4 M 802
04
AC4
SOFTWARE
LEU H:246 , ALA M:1 , ARG M:226
BINDING SITE FOR RESIDUE SO4 M 803
05
AC5
SOFTWARE
TRP M:23 , TYR M:50 , GLY M:52 , ALA M:53 , SER M:54 , SER M:133 , LDA M:704 , HOH M:1030 , HOH M:1066
BINDING SITE FOR RESIDUE SO4 M 804
06
AC6
SOFTWARE
MET L:174 , VAL L:182 , MET L:185 , VAL L:220 , BCB L:302 , HOH L:993 , MET M:120 , VAL M:155 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , BPB M:401 , NS5 M:600 , BCB M:806
BINDING SITE FOR RESIDUE BCB M 805
07
AC7
SOFTWARE
PHE L:97 , MET L:127 , PHE L:128 , VAL L:157 , ASN L:158 , PHE L:160 , GLY L:161 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , LEU L:180 , PHE L:241 , GLY L:244 , THR L:248 , BCB L:304 , BPB L:402 , TYR M:195 , TYR M:208 , BCB M:805 , BCB M:806
BINDING SITE FOR RESIDUE BCB L 302
08
AC8
SOFTWARE
TYR L:162 , PHE L:181 , BCB L:302 , BCB L:304 , GLY M:62 , ALA M:65 , MET M:120 , PHE M:148 , PHE M:154 , VAL M:155 , LEU M:184 , PHE M:187 , 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 , BPB M:401 , BCB M:805
BINDING SITE FOR RESIDUE BCB M 806
09
AC9
SOFTWARE
PHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , VAL L:157 , BCB L:302 , BPB L:402 , TYR M:195 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209 , BCB M:806 , HOH M:991
BINDING SITE FOR RESIDUE BCB L 304
10
BC1
SOFTWARE
PHE L:181 , MET L:185 , VAL L:220 , CEB L:502 , PHE M:59 , GLY M:62 , SER M:123 , LEU M:124 , TRP M:127 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271 , MET M:275 , BCB M:805 , BCB M:806
BINDING SITE FOR RESIDUE BPB M 401
11
BC2
SOFTWARE
PHE L:97 , TRP L:100 , GLU L:104 , VAL L:117 , PHE L:121 , PRO L:124 , TYR L:148 , ALA L:237 , PHE L:241 , BCB L:302 , BCB L:304 , TYR M:208 , LEU M:212 , TRP M:250 , MQ7 M:501
BINDING SITE FOR RESIDUE BPB L 402
12
BC3
SOFTWARE
TYR L:29 , ILE L:39 , TRP L:100 , BPB L:402 , HIS M:217 , THR M:220 , ALA M:246 , TRP M:250 , ALA M:258 , PHE M:270
BINDING SITE FOR RESIDUE MQ7 M 501
13
BC4
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 , LEU C:71 , MET C:74 , THR C:78 , SER C:82 , CYS C:87 , CYS C:90 , HIS C:91 , ALA C:97 , TYR C:104 , ALA C:107 , ARG C:108 , VAL C:212
BINDING SITE FOR RESIDUE HEM C 337
14
BC5
SOFTWARE
TYR C:89 , TYR C:102 , VAL C:106 , MET C:110 , MET C:113 , THR C:114 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , LEU C:289 , ARG C:293 , PRO C:301
BINDING SITE FOR RESIDUE HEM C 338
15
BC6
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 , ARG C:272 , HOH C:937 , HOH C:938 , HOH C:940 , HOH C:973 , ILE M:189
BINDING SITE FOR RESIDUE HEM C 339
16
BC7
SOFTWARE
HIS C:124 , THR C:128 , GLY C:129 , ILE C:236 , LEU C:240 , GLN C:263 , ILE C:266 , GLY C:270 , ILE C:271 , MET C:273 , VAL C:274 , ASP C:304 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315 , HOH C:967 , HOH C:1208
BINDING SITE FOR RESIDUE HEM C 340
17
BC8
SOFTWARE
GLY M:117 , THR M:121 , GLY M:159 , CYS M:160 , VAL M:173 , GLY M:176 , BCB M:805
BINDING SITE FOR RESIDUE NS5 M 600
18
BC9
SOFTWARE
GLU L:212 , ASN L:213 , PHE L:216 , VAL L:220 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , ALA L:226 , BPB M:401
BINDING SITE FOR RESIDUE CEB L 502
19
CC1
SOFTWARE
ARG H:33 , PRO H:54 , ASP H:56 , PHE M:256
BINDING SITE FOR RESIDUE LDA H 701
20
CC2
SOFTWARE
TRP H:17 , ASP L:60 , PHE L:62 , TYR M:195 , CYS M:296 , HIS M:299 , ALA M:301
BINDING SITE FOR RESIDUE LDA L 702
21
CC3
SOFTWARE
PRO H:42 , VAL H:59 , TYR H:60 , LEU H:62 , PRO H:63 , PRO H:65 , HOH H:1183
BINDING SITE FOR RESIDUE LDA H 703
22
CC4
SOFTWARE
TRP M:23 , LEU M:122 , SER M:126 , SER M:133 , SO4 M:804
BINDING SITE FOR RESIDUE LDA M 704
23
CC5
SOFTWARE
TYR L:29
BINDING SITE FOR RESIDUE LDA M 705
24
CC6
SOFTWARE
LEU M:67 , PHE M:71 , ASN M:72 , TRP M:112
BINDING SITE FOR RESIDUE LDA M 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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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Label:
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
(5, 5)
Info
All SCOP Domains
1a: SCOP_d6prcc_ (C:)
2a: SCOP_d6prch1 (H:37-258)
3a: SCOP_d6prcl_ (L:)
4a: SCOP_d6prcm_ (M:)
5a: SCOP_d6prch2 (H:1-36)
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Classes
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)
(
)
Folds
(
)
(
)
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
d6prcc_
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
d6prch1
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
:
L (light) subunit
(70)
Rhodopseudomonas viridis [TaxId: 1079]
(10)
3a
d6prcl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodopseudomonas viridis [TaxId: 1079]
(10)
4a
d6prcm_
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)
5a
d6prch2
H:1-36
[
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]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_6prcH02 (H:120-258)
2a: CATH_6prcH01 (H:2-119)
3a: CATH_6prcC02 (C:145-314)
3b: CATH_6prcC01 (C:1-144,C:315-332)
4a: CATH_6prcM01 (M:1-143)
4b: CATH_6prcM02 (M:144-302)
4c: CATH_6prcL01 (L:1-160)
4d: CATH_6prcL02 (L:161-273)
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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)
Blastochloris viridis. Organism_taxid: 1079.
(10)
1a
6prcH02
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.
(10)
2a
6prcH01
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.
(10)
3a
6prcC02
C:145-314
3b
6prcC01
C:1-144,C:315-332
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.
(10)
4a
6prcM01
M:1-143
4b
6prcM02
M:144-302
4c
6prcL01
L:1-160
4d
6prcL02
L:161-273
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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