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1EYS
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (204 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM
Authors
:
T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, K. Miki
Date
:
08 May 00 (Deposition) - 13 Dec 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Membrane Protein Complex, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, K. Miki
Crystal Structures Of Photosynthetic Reaction Center And High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum: Thermostability And Electron Transfer.
Proc. Natl. Acad. Sci. Usa V. 97 13561 2000
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(9, 21)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
2a: B-2-OCTYLGLUCOSIDE (BGLa)
2b: B-2-OCTYLGLUCOSIDE (BGLb)
2c: B-2-OCTYLGLUCOSIDE (BGLc)
2d: B-2-OCTYLGLUCOSIDE (BGLd)
2e: B-2-OCTYLGLUCOSIDE (BGLe)
2f: B-2-OCTYLGLUCOSIDE (BGLf)
3a: BACTERIOPHEOPHYTIN A (BPHa)
3b: BACTERIOPHEOPHYTIN A (BPHb)
4a: SPIRILLOXANTHIN (CRTa)
5a: FE (III) ION (FEa)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
6d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
7a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
8a: MENAQUINONE 8 (MQ8a)
9a: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHA... (PEFa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BGL
6
Ligand/Ion
B-2-OCTYLGLUCOSIDE
3
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
4
CRT
1
Ligand/Ion
SPIRILLOXANTHIN
5
FE
1
Ligand/Ion
FE (III) ION
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
LDA
1
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
MQ8
1
Ligand/Ion
MENAQUINONE 8
9
PEF
1
Ligand/Ion
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU L:183 , SER L:186
BINDING SITE FOR RESIDUE BGL L 701
02
AC2
SOFTWARE
TYR C:152 , PHE M:72 , ASN M:73 , ALA M:76 , TRP M:80 , TRP M:113
BINDING SITE FOR RESIDUE BGL M 702
03
AC3
SOFTWARE
ASN L:68 , LEU L:69 , TRP L:70 , BGL L:704
BINDING SITE FOR RESIDUE BGL L 703
04
AC4
SOFTWARE
GLN H:13 , ILE H:16 , TRP H:20 , TRP L:70 , BCL L:604 , BGL L:703 , MET M:302
BINDING SITE FOR RESIDUE BGL L 704
05
AC5
SOFTWARE
TRP M:129
BINDING SITE FOR RESIDUE BGL M 705
06
AC6
SOFTWARE
PHE H:22 , TYR H:29 , TRP M:270 , HOH M:930
BINDING SITE FOR RESIDUE BGL M 706
07
AC7
SOFTWARE
HIS L:198 , HIS L:238 , HIS M:218 , GLU M:233 , HIS M:265
BINDING SITE FOR RESIDUE FE M 607
08
AC8
SOFTWARE
HIS L:176 , MET L:182 , ILE L:185 , SER L:186 , PHE L:189 , THR L:190 , VAL L:228 , BCL L:602 , HOH L:914 , TRP M:128 , ILE M:178 , HIS M:181 , LEU M:182 , BCL M:603 , BPH M:605 , CRT M:613
BINDING SITE FOR RESIDUE BCL M 601
09
AC9
SOFTWARE
PHE L:105 , ALA L:132 , ALA L:135 , TYR L:136 , LEU L:139 , VAL L:165 , TYR L:170 , PHE L:175 , HIS L:176 , HIS L:181 , ALA L:184 , ILE L:185 , PHE L:188 , SER L:252 , CYS L:255 , ILE L:256 , BCL L:604 , TYR M:209 , BCL M:601 , BCL M:603
BINDING SITE FOR RESIDUE BCL L 602
10
BC1
SOFTWARE
PHE L:189 , BCL L:602 , BCL L:604 , ILE M:70 , ALA M:152 , PHE M:155 , THR M:185 , SER M:189 , LEU M:195 , TYR M:196 , HIS M:201 , SER M:204 , ILE M:205 , TYR M:209 , ALA M:279 , ILE M:283 , BCL M:601 , BPH M:605 , CRT M:613
BINDING SITE FOR RESIDUE BCL M 603
11
BC2
SOFTWARE
TYR L:136 , PHE L:154 , ILE L:158 , HIS L:161 , LEU L:162 , BCL L:602 , BPH L:606 , BGL L:704 , MET M:202 , ILE M:205 , ALA M:206 , TYR M:209 , BCL M:603 , HOH M:897
BINDING SITE FOR RESIDUE BCL L 604
12
BC3
SOFTWARE
PHE L:189 , CYS L:192 , LEU L:193 , SER L:196 , ILE L:227 , VAL L:228 , LEU M:64 , ILE M:125 , TRP M:128 , PHE M:149 , VAL M:276 , BCL M:601 , BCL M:603
BINDING SITE FOR RESIDUE BPH M 605
13
BC4
SOFTWARE
ILE L:49 , PHE L:105 , TRP L:108 , GLU L:112 , VAL L:125 , PHE L:129 , PHE L:131 , TYR L:156 , ALA L:249 , BCL L:604 , TYR M:209 , ALA M:212 , LEU M:213 , MET M:217 , MET M:255 , MQ8 M:608
BINDING SITE FOR RESIDUE BPH L 606
14
BC5
SOFTWARE
PEF H:708 , PHE L:29 , GLY L:35 , PHE L:39 , TRP L:108 , BPH L:606 , LEU M:213 , MET M:217 , HIS M:218 , THR M:221 , TRP M:251 , ASN M:258 , ALA M:259 , THR M:260 , TRP M:267
BINDING SITE FOR RESIDUE MQ8 M 608
15
BC6
SOFTWARE
TYR C:54 , GLN C:55 , SER C:56 , VAL C:57 , GLN C:58 , VAL C:59 , LEU C:60 , PHE C:68 , MET C:72 , VAL C:75 , THR C:76 , CYS C:85 , CYS C:88 , HIS C:89 , ALA C:95 , LYS C:102 , SER C:105 , ARG C:106 , VAL C:168 , ALA C:171 , SER C:172
BINDING SITE FOR RESIDUE HEM C 609
16
BC7
SOFTWARE
VAL C:75 , TYR C:87 , TYR C:100 , THR C:101 , VAL C:104 , SER C:105 , MET C:108 , CYS C:130 , CYS C:133 , HIS C:134 , PRO C:138 , VAL C:139 , LEU C:269 , ARG C:273 , LEU C:281 , VAL C:283
BINDING SITE FOR RESIDUE HEM C 610
17
BC8
SOFTWARE
ILE C:188 , ARG C:189 , ILE C:190 , THR C:191 , PHE C:211 , MET C:214 , SER C:218 , GLY C:224 , CYS C:225 , CYS C:228 , HIS C:229 , PHE C:234 , ASN C:235 , ARG C:244 , ALA C:247 , TRP C:248 , ARG C:252 , HOH C:877 , HOH C:879 , ILE M:190 , TYR M:316
BINDING SITE FOR RESIDUE HEM C 611
18
BC9
SOFTWARE
HIS C:122 , VAL C:123 , THR C:126 , GLY C:127 , VAL C:128 , ILE C:217 , LYS C:243 , THR C:246 , ALA C:250 , VAL C:254 , VAL C:283 , SER C:284 , CYS C:285 , CYS C:288 , HIS C:289 , ASN C:293 , LYS C:294 , PRO C:295
BINDING SITE FOR RESIDUE HEM C 612
19
CC1
SOFTWARE
ILE M:67 , GLY M:71 , PHE M:72 , PHE M:89 , ILE M:105 , TRP M:114 , LEU M:115 , GLY M:118 , LEU M:119 , THR M:122 , TYR M:156 , PHE M:161 , VAL M:174 , GLY M:177 , HIS M:181 , BCL M:601 , BCL M:603
BINDING SITE FOR RESIDUE CRT M 613
20
CC2
SOFTWARE
ARG L:84 , MET L:85 , GLN L:95 , THR L:98 , VAL L:140 , TRP L:150
BINDING SITE FOR RESIDUE LDA L 707
21
CC3
SOFTWARE
ARG H:31 , LYS H:35 , TYR H:39 , PHE L:29 , PHE M:207 , ARG M:252 , MET M:255 , GLY M:256 , PHE M:257 , MQ8 M:608
BINDING SITE FOR RESIDUE PEF H 708
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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
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
(5, 5)
Info
All SCOP Domains
1a: SCOP_d1eysc_ (C:)
2a: SCOP_d1eysh1 (H:59-259)
3a: SCOP_d1eysl_ (L:)
4a: SCOP_d1eysm_ (M:)
5a: SCOP_d1eysh2 (H:7-43)
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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)
Thermochromatium tepidum [TaxId: 1050]
(1)
1a
d1eysc_
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)
Thermochromatium tepidum [TaxId: 1050]
(1)
2a
d1eysh1
H:59-259
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)
Thermochromatium tepidum [TaxId: 1050]
(1)
3a
d1eysl_
L:
Protein domain
:
M (medium) subunit
(70)
Thermochromatium tepidum [TaxId: 1050]
(1)
4a
d1eysm_
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)
Thermochromatium tepidum [TaxId: 1050]
(1)
5a
d1eysh2
H:7-43
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1eysH02 (H:119-258)
2a: CATH_1eysH01 (H:7-118)
3a: CATH_1eysC02 (C:141-192,C:202-293)
3b: CATH_1eysC01 (C:23-140,C:294-310)
4a: CATH_1eysM01 (M:1-142)
4b: CATH_1eysM02 (M:143-301)
4c: CATH_1eysL01 (L:1-171)
4d: CATH_1eysL02 (L:172-271)
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)
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)
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)
(
)
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)
Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050.
(1)
1a
1eysH02
H:119-258
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)
Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050.
(1)
2a
1eysH01
H:7-118
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)
Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050.
(1)
3a
1eysC02
C:141-192,C:202-293
3b
1eysC01
C:23-140,C:294-310
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050. Thermochromatium tepidum. Organism_taxid: 1050.
(1)
4a
1eysM01
M:1-142
4b
1eysM02
M:143-301
4c
1eysL01
L:1-171
4d
1eysL02
L:172-271
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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