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2ACZ
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (511 KB)
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(1)
Title
:
COMPLEX II (SUCCINATE DEHYDROGENASE) FROM E. COLI WITH ATPENIN A5 INHIBITOR CO-CRYSTALLIZED AT THE UBIQUINONE BINDING SITE
Authors
:
R. Horsefield, V. Yankovskaya, G. Sexton, W. Whittingham, K. Shiomi, S B. Byrne, G. Cecchini, S. Iwata
Date
:
19 Jul 05 (Deposition) - 03 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (3x)
Keywords
:
Membrane Protein, Aerobic Reparatory Complex Ii, Sqr, Succinate:Ubiquinone Oxidoreductase, Aa5, At5, Atpenin A5, Sdh, Succinate Dehydrogenase, Oxidoreductase-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Horsefield, V. Yankovskaya, G. Sexton, W. Whittingham, K. Shiomi, S. Omura, B. Byrne, G. Cecchini, S. Iwata
Structural And Computational Analysis Of The Quinone-Bindin Site Of Complex Ii (Succinate-Ubiquinone Oxidoreductase): A Mechanism Of Electron Transfer And Proton Conduction During Ubiquinone Reduction.
J. Biol. Chem. V. 281 7309 2006
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Hetero Components
(8, 8)
Info
All Hetero Components
1a: 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIM... (AT5a)
2a: CARDIOLIPIN (CDNa)
3a: FE3-S4 CLUSTER (F3Sa)
4a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
5a: FE2/S2 (INORGANIC) CLUSTER (FESa)
6a: HEME B/C (HEBa)
7a: OXALOACETATE ION (OAAa)
8a: IRON/SULFUR CLUSTER (SF4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AT5
1
Ligand/Ion
3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE
2
CDN
1
Ligand/Ion
CARDIOLIPIN
3
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
4
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
5
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
6
HEB
1
Ligand/Ion
HEME B/C
7
OAA
1
Ligand/Ion
OXALOACETATE ION
8
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:51 , PHE A:126 , HIS A:242 , LEU A:252 , THR A:254 , GLU A:255 , ARG A:286 , HIS A:354 , ARG A:399 , GLY A:401 , GLY A:402 , FAD A:601
BINDING SITE FOR RESIDUE OAA A 589
2
AC2
SOFTWARE
GLY A:14 , ALA A:15 , GLY A:16 , GLY A:17 , ALA A:18 , SER A:37 , LYS A:38 , VAL A:39 , SER A:44 , HIS A:45 , THR A:46 , SER A:48 , ALA A:49 , GLN A:50 , GLY A:51 , GLY A:52 , TRP A:164 , TYR A:165 , ALA A:166 , ALA A:201 , THR A:202 , GLY A:203 , ASN A:214 , ASP A:221 , TYR A:355 , GLU A:388 , ARG A:399 , GLY A:402 , SER A:404 , LEU A:405 , LEU A:408 , OAA A:589
BINDING SITE FOR RESIDUE FAD A 601
3
AC3
SOFTWARE
SER B:54 , CYS B:55 , ARG B:56 , GLY B:58 , VAL B:59 , CYS B:60 , GLY B:61 , ASP B:63 , CYS B:75
BINDING SITE FOR RESIDUE FES B 302
4
AC4
SOFTWARE
CYS B:149 , ILE B:150 , CYS B:152 , ALA B:153 , CYS B:154 , CYS B:155 , CYS B:216 , PRO B:217
BINDING SITE FOR RESIDUE SF4 B 303
5
AC5
SOFTWARE
CYS B:159 , PRO B:172 , CYS B:206 , HIS B:207 , SER B:208 , ILE B:209 , MET B:210 , ASN B:211 , CYS B:212 , THR B:223
BINDING SITE FOR RESIDUE F3S B 304
6
AC6
SOFTWARE
HIS B:207 , HIS C:30 , ARG C:31 , THR C:37 , PHE C:38 , HIS C:84 , VAL C:85 , GLY C:88 , CDN C:132 , ARG D:20 , ALA D:23 , THR D:27 , ILE D:68 , HIS D:71 , GLY D:75 , MET D:76 , GLN D:78
BINDING SITE FOR RESIDUE HEB C 130
7
AC7
SOFTWARE
PRO B:160 , TRP B:164 , HIS B:207 , ILE B:209 , LEU C:15 , PHE C:20 , ALA C:24 , SER C:27 , ILE C:28 , ARG C:31 , ASP D:82 , TYR D:83
BINDING SITE FOR RESIDUE AT5 C 131
8
AC8
SOFTWARE
LEU C:44 , SER C:51 , ALA C:61 , SER C:62 , MET C:65 , MET C:74 , LEU C:78 , VAL C:115 , LEU C:123 , ALA C:124 , VAL C:126 , LEU C:127 , TRP C:129 , HEB C:130 , ILE D:30 , GLY D:41 , LEU D:43 , ILE D:68
BINDING SITE FOR RESIDUE CDN C 132
[
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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
(6, 6)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:8-97)
2: SDH_CYT_1 (C:9-33)
3: FRD_SDH_FAD_BINDING (A:43-52,A:43-52,A:43-52)
4: SDH_CYT_2 (C:84-97)
5: 4FE4S_FER_2 (B:139-169)
6: 4FE4S_FER_1 (B:149-160)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
SDHB_ECOLI
8-97
1
B:8-97
2
SDH_CYT_1
PS01000
Succinate dehydrogenase cytochrome b subunit signature 1.
DHSC_ECOLI
9-33
1
C:9-33
3
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_ECO57
43-52
1
A:43-52
SDHA_ECOL6
43-52
1
A:43-52
SDHA_ECOLI
43-52
1
A:43-52
4
SDH_CYT_2
PS01001
Succinate dehydrogenase cytochrome b subunit signature 2.
DHSC_ECOLI
84-97
1
C:84-97
5
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_ECOLI
139-169
1
B:139-169
6
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_ECOLI
149-160
1
B:149-160
[
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Exons
(0, 0)
Info
All Exons
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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_d2aczb1 (B:107-238)
2a: SCOP_d2aczb2 (B:1-106)
3a: SCOP_d2aczc_ (C:)
4a: SCOP_d2aczd1 (D:3-115)
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
alpha-helical ferredoxin
(43)
Family
:
Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
(35)
Protein domain
:
automated matches
(8)
Escherichia coli [TaxId: 562]
(2)
1a
d2aczb1
B:107-238
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
automated matches
(14)
Escherichia coli [TaxId: 562]
(2)
2a
d2aczb2
B:1-106
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(55)
Family
:
Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
(48)
Protein domain
:
Succinate dehydrogenase subunit SdhC
(7)
Escherichia coli [TaxId: 562]
(7)
3a
d2aczc_
C:
Protein domain
:
Succinate dehydrogenase subunit SdhD
(6)
Escherichia coli [TaxId: 562]
(6)
4a
d2aczd1
D:3-115
[
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]
CATH Domains
(6, 7)
Info
all CATH domains
1a: CATH_2aczA01 (A:1-245,A:351-430)
2a: CATH_2aczB01 (B:1-106)
3a: CATH_2aczA04 (A:548-588)
4a: CATH_2aczB02 (B:107-238)
5a: CATH_2aczC00 (C:1-129)
5b: CATH_2aczD01 (D:11-115)
6a: CATH_2aczA03 (A:431-547)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Escherichia coli. Organism_taxid: 562.
(12)
1a
2aczA01
A:1-245,A:351-430
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Escherichia coli. Organism_taxid: 562.
(14)
2a
2aczB01
B:1-106
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
succinate dehydrogenase protein domain
(23)
Escherichia coli. Organism_taxid: 562.
(10)
3a
2aczA04
A:548-588
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Homologous Superfamily
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Escherichia coli. Organism_taxid: 562.
(10)
4a
2aczB02
B:107-238
Architecture
:
Up-down Bundle
(3216)
Topology
:
3 helical TM bundles of succinate and fumarate reductases
(23)
Homologous Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(23)
Escherichia coli. Organism_taxid: 562.
(10)
5a
2aczC00
C:1-129
5b
2aczD01
D:11-115
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.100, no name defined]
(37)
Escherichia coli. Organism_taxid: 562.
(10)
6a
2aczA03
A:431-547
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (183 KB)
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