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3AEF
Asym. Unit
Info
Asym.Unit (369 KB)
Biol.Unit 1 (359 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II WITH AN EMPTY QUINONE-BINDING POCKET
Authors
:
S. Harada, T. Sasaki, M. Shindo, Y. Kido, D. K. Inaoka, J. Omori, A. Osana K. Sakamoto, J. Mao, S. Matsuoka, M. Inoue, T. Honma, A. Tanaka, K. Kita
Date
:
04 Feb 10 (Deposition) - 09 Feb 11 (Release) - 09 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Respiratory Complex Ii, Inhibitors, Electron Transport, Iron, Iron- Sulfur, Metal-Binding, Mitochondrion, Mitochondrion Inner Membrane, Oxidoreductase, Transit Peptide, Transport, Tricarboxylic Acid Cycle, Heme, Transmembrane, Fad-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Harada, T. Sasaki, M. Shindo, Y. Kido, D. K. Inaoka, J. Omori, A. Osanai, K. Sakamoto, J. Mao, S. Matsuoka, M. Inoue, T. Honma, A. Tanaka, K. Kita
Crystal Structure Of Porcine Heart Mitochondrial Complex Ii With An Empty Quinone-Binding Pocket
To Be Published
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Hetero Components
(6, 6)
Info
All Hetero Components
1a: L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-G... (EPHa)
2a: FE3-S4 CLUSTER (F3Sa)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6a: IRON/SULFUR CLUSTER (SF4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
EPH
1
Ligand/Ion
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:26 , ALA A:27 , GLY A:28 , GLY A:29 , ALA A:30 , VAL A:48 , THR A:49 , LYS A:50 , LEU A:51 , SER A:56 , HIS A:57 , THR A:58 , ALA A:60 , ALA A:61 , GLN A:62 , GLY A:63 , GLY A:64 , TYR A:177 , PHE A:178 , ALA A:179 , ALA A:213 , THR A:214 , GLY A:215 , THR A:225 , ASP A:233 , LEU A:264 , HIS A:365 , TYR A:366 , GLY A:397 , GLU A:398 , ARG A:409 , ALA A:412 , ASN A:413 , SER A:414 , LEU A:415 , LEU A:418
BINDING SITE FOR RESIDUE FAD A 700
2
AC2
SOFTWARE
SER B:64 , CYS B:65 , ARG B:66 , GLY B:68 , CYS B:70 , GLY B:71 , CYS B:73 , CYS B:85
BINDING SITE FOR RESIDUE FES B 302
3
AC3
SOFTWARE
CYS B:158 , ILE B:159 , CYS B:161 , ALA B:162 , CYS B:164 , CYS B:225 , PRO B:226 , LYS B:227 , PRO B:231
BINDING SITE FOR RESIDUE SF4 B 303
4
AC4
SOFTWARE
CYS B:168 , TYR B:178 , CYS B:215 , HIS B:216 , ILE B:218 , MET B:219 , ASN B:220 , CYS B:221 , ILE B:235
BINDING SITE FOR RESIDUE F3S B 304
5
AC5
SOFTWARE
HIS B:216 , HIS C:45 , ARG C:46 , GLY C:49 , LEU C:52 , SER C:53 , VAL C:56 , HIS C:101 , THR C:102 , HIS C:108 , SER D:50 , LEU D:53 , LEU D:54 , HIS D:79 , GLY D:83
BINDING SITE FOR RESIDUE HEM C 1305
6
AC6
SOFTWARE
PHE C:59 , TYR D:61 , PRO D:64 , TRP D:134
BINDING SITE FOR RESIDUE EPH D 1306
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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
(7, 7)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:12-103)
2: SDH_CYT_1 (C:24-48)
3: 2FE2S_FER_1 (B:65-73)
4: FRD_SDH_FAD_BINDING (A:55-64)
5: SDH_CYT_2 (C:101-114)
6: 4FE4S_FER_2 (B:148-178)
7: 4FE4S_FER_1 (B:158-169)
;
View:
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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_PIG
40-131
1
B:12-103
2
SDH_CYT_1
PS01000
Succinate dehydrogenase cytochrome b subunit signature 1.
C560_PIG
50-74
1
C:24-48
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
SDHB_PIG
93-101
1
B:65-73
4
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_PIG
97-106
1
A:55-64
5
SDH_CYT_2
PS01001
Succinate dehydrogenase cytochrome b subunit signature 2.
C560_PIG
127-140
1
C:101-114
6
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_PIG
176-206
1
B:148-178
7
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_PIG
186-197
1
B:158-169
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(7, 7)
Info
All SCOP Domains
1a: SCOP_d3aefb2 (B:115-247)
2a: SCOP_d3aefa3 (A:446-622)
3a: SCOP_d3aefb1 (B:9-114)
4a: SCOP_d3aefa2 (A:274-360)
5a: SCOP_d3aefa1 (A:10-273,A:361-445)
6a: SCOP_d3aefc_ (C:)
7a: SCOP_d3aefd_ (D:)
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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)
Pig (Sus scrofa) [TaxId: 9823]
(5)
1a
d3aefb2
B:115-247
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)
Pig (Sus scrofa) [TaxId: 9823]
(5)
2a
d3aefa3
A:446-622
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)
Pig (Sus scrofa) [TaxId: 9823]
(5)
3a
d3aefb1
B:9-114
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)
Pig (Sus scrofa) [TaxId: 9823]
(5)
4a
d3aefa2
A:274-360
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)
Pig (Sus scrofa) [TaxId: 9823]
(5)
5a
d3aefa1
A:10-273,A:361-445
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
:
Large cytochrome binding protein CybL
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
6a
d3aefc_
C:
Protein domain
:
Small cytochrome binding protein CybS
(5)
Pig (Sus scrofa) [TaxId: 9823]
(5)
7a
d3aefd_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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Asymmetric Unit 1
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