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3V3Z
Asym. Unit
Info
Asym.Unit (157 KB)
Biol.Unit 1 (147 KB)
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(1)
Title
:
I(L177)H MUTANT STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
Authors
:
A. G. Gabdulkhakov, T. Y. Fufina, L. G. Vasilieva, V. A. Shuvalov
Date
:
14 Dec 11 (Deposition) - 14 Mar 12 (Release) - 27 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Photosynthetic Reaction Center, Primary Electron Donor, Membrane, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. G. Vasilieva, T. Y. Fufina, A. G. Gabdulkhakov, M. M. Leonova, R. A. Khatypov, V. A. Shuvalov
The Site-Directed Mutation I(L177)H In Rhodobacter Sphaeroides Reaction Center Affects Coordination Of P(A) An B(B) Bacteriochlorophylls.
Biochim. Biophys. Acta V. 1817 1407 2012
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Hetero Components
(11, 27)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL A (BCLa)
01b: BACTERIOCHLOROPHYLL A (BCLb)
01c: BACTERIOCHLOROPHYLL A (BCLc)
01d: BACTERIOCHLOROPHYLL A (BCLd)
02a: BACTERIOPHEOPHYTIN A (BPHa)
02b: BACTERIOPHEOPHYTIN A (BPHb)
03a: CHLORIDE ION (CLa)
04a: 1,4-DIETHYLENE DIOXIDE (DIOa)
04b: 1,4-DIETHYLENE DIOXIDE (DIOb)
05a: FE (III) ION (FEa)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
06b: HEPTANE-1,2,3-TRIOL (HTOb)
06c: HEPTANE-1,2,3-TRIOL (HTOc)
07a: POTASSIUM ION (Ka)
08a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
08b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
08c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
08d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
08e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
09a: PHOSPHATE ION (PO4a)
09b: PHOSPHATE ION (PO4b)
09c: PHOSPHATE ION (PO4c)
09d: PHOSPHATE ION (PO4d)
09e: PHOSPHATE ION (PO4e)
10a: SPEROIDENONE (SPNa)
11a: UBIQUINONE-10 (U10a)
11b: UBIQUINONE-10 (U10b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CL
1
Ligand/Ion
CHLORIDE ION
4
DIO
2
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
5
FE
1
Ligand/Ion
FE (III) ION
6
HTO
3
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
K
1
Ligand/Ion
POTASSIUM ION
8
LDA
5
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
9
PO4
5
Ligand/Ion
PHOSPHATE ION
10
SPN
1
Ligand/Ion
SPEROIDENONE
11
U10
2
Ligand/Ion
UBIQUINONE-10
[
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]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU H:27 , PO4 M:800
BINDING SITE FOR RESIDUE LDA H 704
02
AC2
SOFTWARE
HIS H:126 , TYR L:73 , LYS L:82 , THR M:21
BINDING SITE FOR RESIDUE PO4 H 803
03
AC3
SOFTWARE
ARG H:202
BINDING SITE FOR RESIDUE PO4 H 804
04
AC4
SOFTWARE
ASP H:82 , ALA H:116
BINDING SITE FOR RESIDUE HTO H 2
05
AC5
SOFTWARE
HIS H:128 , ASN H:129 , LYS H:132
BINDING SITE FOR RESIDUE HTO H 3
06
AC6
SOFTWARE
ARG H:177 , PHE H:178 , GLN H:194 , GLU H:230 , CYS H:234 , GLY M:230 , ARG M:233
BINDING SITE FOR RESIDUE DIO H 251
07
AC7
SOFTWARE
MET H:134 , ALA H:137 , PHE H:140
BINDING SITE FOR RESIDUE K H 1
08
AC8
SOFTWARE
HIS L:168 , MET L:174 , HIS L:177 , THR L:178 , THR L:182 , HOH L:297 , MET M:122 , LEU M:160 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:303 , BPH M:401 , SPN M:600
BINDING SITE FOR RESIDUE BCL L 301
09
AC9
SOFTWARE
PHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , TYR L:128 , LEU L:131 , VAL L:157 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , HIS L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:304 , BPH L:402 , TYR M:210 , BCL M:303
BINDING SITE FOR RESIDUE BCL L 302
10
BC1
SOFTWARE
TYR L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:302 , BPH L:402 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BCL M:303 , LDA M:701
BINDING SITE FOR RESIDUE BCL L 304
11
BC2
SOFTWARE
ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , ALA L:124 , TYR L:128 , HIS L:153 , VAL L:241 , BCL L:302 , BCL L:304 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252
BINDING SITE FOR RESIDUE BPH L 402
12
BC3
SOFTWARE
ILE L:175 , HIS L:190 , LEU L:193 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229
BINDING SITE FOR RESIDUE U10 L 502
13
BC4
SOFTWARE
GLU H:43 , ASP H:46 , SER L:4 , ARG L:7
BINDING SITE FOR RESIDUE HTO L 282
14
BC5
SOFTWARE
PHE L:181 , BCL L:301 , BCL L:302 , BCL L:304 , ALA M:153 , LEU M:156 , THR M:186 , ASN M:187 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , LEU M:209 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BPH M:401
BINDING SITE FOR RESIDUE BCL M 303
15
BC6
SOFTWARE
PHE L:181 , LEU L:185 , LEU L:189 , BCL L:301 , LEU M:60 , GLY M:63 , VAL M:126 , TRP M:129 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:303
BINDING SITE FOR RESIDUE BPH M 401
16
BC7
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M 500
17
BC8
SOFTWARE
GLY L:35 , TRP L:100 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , ILE M:265 , TRP M:268 , LDA M:702
BINDING SITE FOR RESIDUE U10 M 501
18
BC9
SOFTWARE
BCL L:301 , PHE M:67 , PHE M:68 , GLY M:71 , TRP M:75 , PHE M:105 , TRP M:115 , SER M:119 , MET M:122 , TRP M:157 , GLY M:161 , GLY M:178 , HIS M:182
BINDING SITE FOR RESIDUE SPN M 600
19
CC1
SOFTWARE
BCL L:304 , PRO M:200 , LDA M:702
BINDING SITE FOR RESIDUE LDA M 701
20
CC2
SOFTWARE
GLN H:32 , TYR H:40 , PHE H:56 , ARG M:253 , GLY M:257 , U10 M:501 , LDA M:701
BINDING SITE FOR RESIDUE LDA M 702
21
CC3
SOFTWARE
TRP M:148 , TRP M:271 , PO4 M:800
BINDING SITE FOR RESIDUE LDA M 703
22
CC4
SOFTWARE
THR M:8 , TRP M:41
BINDING SITE FOR RESIDUE LDA M 705
23
CC5
SOFTWARE
LDA H:704 , ASN L:199 , HIS M:145 , ARG M:267 , LDA M:703
BINDING SITE FOR RESIDUE PO4 M 800
24
CC6
SOFTWARE
GLU L:201 , LYS M:144
BINDING SITE FOR RESIDUE PO4 M 801
25
CC7
SOFTWARE
ASN M:28 , GLY M:53 , SER M:54
BINDING SITE FOR RESIDUE PO4 M 802
26
CC8
SOFTWARE
GLN M:4 , ASN M:5 , ILE M:6
BINDING SITE FOR RESIDUE CL M 304
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,M:195-221)
;
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_RHOSH
167-193
1
L:166-192
RCEM_RHOSH
196-222
1
M:195-221
[
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Exons
(0, 0)
Info
All Exons
View:
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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, 4)
Info
All SCOP Domains
1a: SCOP_d3v3zh2 (H:36-250)
2a: SCOP_d3v3zl_ (L:)
3a: SCOP_d3v3zm_ (M:)
4a: SCOP_d3v3zh1 (H:10-35)
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Classes
(
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(
)
Folds
(
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(
)
Superfamilies
(
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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
d3v3zh2
H:36-250
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
d3v3zl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d3v3zm_
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)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
4a
d3v3zh1
H:10-35
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Atom Selection
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Protein
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Sidechain
Hetero
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain H
Chain L
Chain M
Asymmetric Unit 1
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