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Asym. Unit
Info
Asym.Unit (186 KB)
Biol.Unit 1 (179 KB)
Biol.Unit 2 (523 KB)
Biol.Unit 3 (352 KB)
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(1)
Title
:
COMPLEX II (SUCCINATE DEHYDROGENASE) FROM E. COLI WITH UBIQUINONE BOUND
Authors
:
V. Yankovskaya, R. Horsefield, S. Tornroth, C. Luna-Chavez, H. Miyoshi, C. Leger, B. Byrne, G. Cecchini, S. Iwata
Date
:
11 Dec 02 (Deposition) - 25 Feb 03 (Release) - 31 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (3x)
Biol. Unit 3: A,B,C,D (2x)
Keywords
:
Membrane Protein, Oxygen Respiratory Chain, Oxidoreductase/Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Yankovskaya, R. Horsefield, S. Tornroth, C. Luna-Chavez, H. Miyoshi, C. Leger, B. Byrne, G. Cecchini, S. Iwata
Architecture Of Succinate Dehydrogenase And Reactive Oxygen Species Generation.
Science V. 299 700 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(10, 11)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
01b: CALCIUM ION (CAb)
02a: CARDIOLIPIN (CDNa)
03a: L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-G... (EPHa)
04a: FE3-S4 CLUSTER (F3Sa)
05a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
06a: FE2/S2 (INORGANIC) CLUSTER (FESa)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
08a: OXALOACETATE ION (OAAa)
09a: IRON/SULFUR CLUSTER (SF4a)
10a: UBIQUINONE-2 (UQ2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CDN
1
Ligand/Ion
CARDIOLIPIN
3
EPH
1
Ligand/Ion
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
4
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
5
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
7
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
OAA
1
Ligand/Ion
OXALOACETATE ION
9
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
10
UQ2
1
Ligand/Ion
UBIQUINONE-2
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:51 , PHE A:126 , HIS A:242 , THR A:254 , GLU A:255 , ARG A:286 , HIS A:354 , ARG A:399 , GLY A:401 , GLY A:402 , FAD A:601 , HOH A:614
BINDING SITE FOR RESIDUE OAA A 589
02
AC2
SOFTWARE
TYR A:355 , MET A:356 , MET A:357 , GLY A:358 , GLU A:388 , ALA A:390
BINDING SITE FOR RESIDUE CA A 590
03
AC3
SOFTWARE
ASP B:187 , THR B:190
BINDING SITE FOR RESIDUE CA B 311
04
AC4
SOFTWARE
GLY A:14 , ALA A:15 , GLY A:16 , GLY A:17 , ALA A:18 , SER A:37 , LYS A:38 , 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 , THR A:213 , ASN A:214 , ASP A:221 , LEU A:252 , TYR A:355 , GLY A:387 , GLU A:388 , ARG A:399 , GLY A:402 , ASN A:403 , SER A:404 , LEU A:405 , LEU A:408 , OAA A:589 , HOH A:617
BINDING SITE FOR RESIDUE FAD A 601
05
AC5
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
06
AC6
SOFTWARE
CYS B:149 , ILE B:150 , CYS B:152 , ALA B:153 , CYS B:155 , ALA B:173 , CYS B:216 , LEU B:220
BINDING SITE FOR RESIDUE SF4 B 303
07
AC7
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
08
AC8
SOFTWARE
HIS B:207 , HIS C:30 , ARG C:31 , GLY C:34 , THR C:37 , PHE C:38 , HIS C:84 , VAL C:85 , GLY C:88 , ILE C:89 , CDN C:308 , HOH C:311 , 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 HEM C 305
09
AC9
SOFTWARE
TRP B:164 , ILE B:209 , LEU C:15 , PHE C:20 , SER C:27 , ILE C:28 , TYR D:83
BINDING SITE FOR RESIDUE UQ2 D 306
10
BC1
SOFTWARE
VAL C:41 , LEU C:44 , SER C:51 , ALA C:61 , SER C:62 , LEU C:78 , VAL C:115 , LEU C:123 , VAL C:126 , LEU C:127 , TRP C:129 , HEM C:305 , EPH C:309 , ILE D:30 , PHE D:37 , GLY D:41 , LEU D:43 , TRP D:48 , ILE D:68 , HOH D:315
BINDING SITE FOR RESIDUE CDN C 308
11
BC2
SOFTWARE
LYS C:107 , LYS C:111 , TRP C:129 , CDN C:308
BINDING SITE FOR RESIDUE EPH C 309
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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)
4: SDH_CYT_2 (C:84-97)
5: 4FE4S_FER_2 (B:139-169)
6: 4FE4S_FER_1 (B:149-160)
;
View:
Select:
Label:
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_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
[
close PROSITE info
]
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
(7, 7)
Info
All SCOP Domains
1a: SCOP_d1nekb1 (B:107-238)
2a: SCOP_d1neka1 (A:451-588)
3a: SCOP_d1nekb2 (B:1-106)
4a: SCOP_d1neka3 (A:236-355)
5a: SCOP_d1neka2 (A:1-235,A:356-450)
6a: SCOP_d1nekc_ (C:)
7a: SCOP_d1nekd_ (D:)
View:
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Classes
(
)
(
)
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
:
Succinate dehydogenase
(16)
Escherichia coli [TaxId: 562]
(5)
1a
d1nekb1
B:107-238
Fold
:
Spectrin repeat-like
(186)
Superfamily
:
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
(26)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
(26)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
2a
d1neka1
A:451-588
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
:
Succinate dehydogenase iron-sulfur protein, N-terminal domain
(16)
Escherichia coli [TaxId: 562]
(5)
3a
d1nekb2
B:1-106
Fold
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Superfamily
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
4a
d1neka3
A:236-355
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain
(45)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
5a
d1neka2
A:1-235,A:356-450
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)
6a
d1nekc_
C:
Protein domain
:
Succinate dehydrogenase subunit SdhD
(6)
Escherichia coli [TaxId: 562]
(6)
7a
d1nekd_
D:
[
close SCOP info
]
CATH Domains
(7, 8)
Info
all CATH domains
1a: CATH_1nekA01 (A:1-245,A:351-430)
2a: CATH_1nekA02 (A:246-350)
3a: CATH_1nekB01 (B:1-106)
4a: CATH_1nekA04 (A:548-588)
5a: CATH_1nekB02 (B:107-238)
6a: CATH_1nekC00 (C:1-129)
6b: CATH_1nekD01 (D:11-115)
7a: CATH_1nekA03 (A:431-547)
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(
)
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)
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)
(
)
Topologies
(
)
(
)
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.
(10)
1a
1nekA01
A:1-245,A:351-430
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Flavocytochrome C3; Chain A, domain 1
(40)
Homologous Superfamily
:
Flavocytochrome C3; Chain A, domain 1
(40)
Escherichia coli. Organism_taxid: 562.
(6)
2a
1nekA02
A:246-350
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)
3a
1nekB01
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.
(5)
4a
1nekA04
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.
(5)
5a
1nekB02
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.
(5)
6a
1nekC00
C:1-129
6b
1nekD01
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.
(8)
7a
1nekA03
A:431-547
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Sdh_cyt_1nekC01 (C:5-124)
1b: PFAM_Sdh_cyt_1nekD01 (D:3-113)
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Clans
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)
Organisms
(
)
(
)
Clan
:
FumRed-TM
(17)
Family
:
Sdh_cyt
(10)
Escherichia coli (strain K12)
(8)
1a
Sdh_cyt-1nekC01
C:5-124
1b
Sdh_cyt-1nekD01
D:3-113
[
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Asym.Unit (186 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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