PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
3PRC
Biol. Unit 2
Info
Asym.Unit (230 KB)
Biol.Unit 1 (428 KB)
Biol.Unit 2 (217 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)
Authors
:
C. R. D. Lancaster, H. Michel
Date
:
29 Jul 97 (Deposition) - 11 Nov 98 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (2x)
Biol. Unit 2: C,H,L,M (1x)
Keywords
:
Photosynthetic Reaction Center, Secondary Quinone (Qb)-Depleted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. R. Lancaster, H. Michel
The Coupling Of Light-Induced Electron Transfer And Proton Uptake As Derived From Crystal Structures Of Reaction Centres From Rhodopseudomonas Viridis Modified At The Binding Site Of The Secondary Quinone, Qb.
Structure V. 5 1339 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 25)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL B (BCBa)
1b: BACTERIOCHLOROPHYLL B (BCBb)
1c: BACTERIOCHLOROPHYLL B (BCBc)
1d: BACTERIOCHLOROPHYLL B (BCBd)
2a: BACTERIOPHEOPHYTIN B (BPBa)
2b: BACTERIOPHEOPHYTIN B (BPBb)
3a: FE (II) ION (FE2a)
4a: N-FORMYLMETHIONINE (FMEa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
5d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
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)
6g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
7a: MENAQUINONE-7 (MQ7a)
8a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
9a: SULFATE ION (SO4a)
9b: SULFATE ION (SO4b)
9c: SULFATE ION (SO4c)
9d: 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
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
7
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
7
MQ7
1
Ligand/Ion
MENAQUINONE-7
8
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
9
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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 , HOH H:831 , ARG M:251 , HOH M:849
BINDING SITE FOR RESIDUE SO4 H 801
03
AC3
SOFTWARE
HOH H:865 , ASN L:199 , HOH L:769 , HIS M:143 , ARG M:265
BINDING SITE FOR RESIDUE SO4 M 802
04
AC4
SOFTWARE
LEU H:246 , HOH H:872 , ALA M:1 , ARG M:226 , HOH M:876
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:839 , HOH M:850 , HOH M:895
BINDING SITE FOR RESIDUE SO4 M 804
06
AC6
SOFTWARE
HIS L:168 , MET L:174 , VAL L:177 , SER L:178 , PHE L:181 , VAL L:182 , MET L:185 , VAL L:220 , BCB L:302 , HOH L:723 , MET M:120 , VAL M:155 , ILE M:158 , ILE M:177 , HIS M:180 , ILE M:181 , LEU M:184 , BPB M:401 , NS5 M:600 , BCB M:806
BINDING SITE FOR RESIDUE BCB M 805
07
AC7
SOFTWARE
PHE L:97 , 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: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 , MET M:120 , PHE M:148 , PHE M:154 , VAL M:155 , LEU M:184 , 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:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCB L:302 , BPB L:402 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209 , BCB M:806 , HOH M:825
BINDING SITE FOR RESIDUE BCB L 304
10
BC1
SOFTWARE
PHE L:181 , MET L:185 , LEU L:189 , VAL L:220 , 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 , 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 , ALA L:120 , PHE L:121 , PRO L:124 , TYR L:148 , HIS L:153 , 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 , GLY L:35 , ILE L:39 , TRP L:100 , BPB L:402 , HIS M:217 , THR M:220 , ALA M:246 , TRP M:250 , ALA M:258 , ILE M:260 , VAL M:263
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 , 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
ILE C:77 , 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 , VAL C:145 , 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:360 , HOH C:361 , HOH C:362 , HOH C:383 , ILE M:189
BINDING SITE FOR RESIDUE HEM C 339
16
BC7
SOFTWARE
HIS C:124 , THR C:128 , GLY C:129 , LEU C:240 , PHE C:246 , GLN C:263 , ILE C:266 , GLY C:270 , 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:378 , HOH C:445
BINDING SITE FOR RESIDUE HEM C 340
17
BC8
SOFTWARE
ILE M:69 , GLY M:117 , THR M:121 , CYS M:160 , TRP M:169 , VAL M:173 , GLY M:176 , BCB M:805
BINDING SITE FOR RESIDUE NS5 M 600
18
BC9
SOFTWARE
ARG H:33 , ASP H:56
BINDING SITE FOR RESIDUE LDA H 701
19
CC1
SOFTWARE
HOH H:894 , ASP L:60 , PHE L:62 , HOH L:772 , CYS M:296 , HIS M:299 , ALA M:301
BINDING SITE FOR RESIDUE LDA L 702
20
CC2
SOFTWARE
PRO H:42 , VAL H:59 , TYR H:60 , LEU H:62 , PRO H:63 , TYR H:64 , PRO H:65 , ARG H:81
BINDING SITE FOR RESIDUE LDA H 703
21
CC3
SOFTWARE
SER M:126 , SO4 M:804
BINDING SITE FOR RESIDUE LDA M 704
22
CC4
SOFTWARE
TYR L:29 , ILE M:254 , PHE M:256
BINDING SITE FOR RESIDUE LDA M 705
23
CC5
SOFTWARE
PHE M:71 , ASN M:72 , TRP M:112
BINDING SITE FOR RESIDUE LDA M 706
24
CC6
SOFTWARE
PHE L:216 , TYR L:222 , ILE L:224 , HOH L:758 , HOH L:761 , ILE M:41
BINDING SITE FOR RESIDUE LDA L 707
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (C:82-314)
2: REACTION_CENTER (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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 5)
Info
All SCOP Domains
1a: SCOP_d3prcc_ (C:)
2a: SCOP_d3prch1 (H:37-258)
3a: SCOP_d3prcl_ (L:)
4a: SCOP_d3prcm_ (M:)
5a: SCOP_d3prch2 (H:1-36)
View:
Select:
Label:
Classes
(
)
(
)
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
d3prcc_
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
d3prch1
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
d3prcl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodopseudomonas viridis [TaxId: 1079]
(10)
4a
d3prcm_
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
d3prch2
H:1-36
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3prcH02 (H:120-258)
2a: CATH_3prcH01 (H:2-119)
3a: CATH_3prcC02 (C:143-313)
3b: CATH_3prcC01 (C:1-142,C:314-332)
4a: CATH_3prcM01 (M:1-143)
4b: CATH_3prcM02 (M:144-302)
4c: CATH_3prcL01 (L:1-163)
4d: CATH_3prcL02 (L:164-263)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
3prcH02
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
3prcH01
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
3prcC02
C:143-313
3b
3prcC01
C:1-142,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.
(10)
4a
3prcM01
M:1-143
4b
3prcM02
M:144-302
4c
3prcL01
L:1-163
4d
3prcL02
L:164-263
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Chain H
Chain L
Chain M
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (230 KB)
Header - Asym.Unit
Biol.Unit 1 (428 KB)
Header - Biol.Unit 1
Biol.Unit 2 (217 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3PRC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help