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1YQ4
Asym. Unit
Info
Asym.Unit (200 KB)
Biol.Unit 1 (192 KB)
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(1)
Title
:
AVIAN RESPIRATORY COMPLEX II WITH 3-NITROPROPIONATE AND UBIQUINONE
Authors
:
L. Huang, G. Sun, D. Cobessi, A. Wang, J. T. Shen, E. Y. Tung, V. E. Anderso E. A. Berry
Date
:
01 Feb 05 (Deposition) - 20 Dec 05 (Release) - 17 Feb 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.33
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Complex Ii, Membrane Protein, Heme Protein, Iron Sulfur Protein, Cytochrome B, Oxidoreductase, Redox Enzyme, Respiratory Chain, Oxaloacetate Nitropropionate Ubiquinone
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Huang, G. Sun, D. Cobessi, A. C. Wang, J. T. Shen, E. Y. Tung, V. E. Anderson, E. A. Berry
3-Nitropropionic Acid Is A Suicide Inhibitor Of Mitochondrial Respiration That, Upon Oxidation By Complex Ii, Forms A Covalent Adduct With A Catalytic Base Arginine In The Active Site Of The Enzyme
J. Biol. Chem. V. 281 5965 2006
(for further references see the
PDB file header
)
[
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]
Hetero Components
(10, 11)
Info
All Hetero Components
01a: 3-NITROPROPANOIC ACID (3NPa)
02a: FE3-S4 CLUSTER (F3Sa)
03a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
04a: FE2/S2 (INORGANIC) CLUSTER (FESa)
05a: GLYCEROL (GOLa)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07a: HEXYL BETA-D-GLUCOPYRANOSIDE (JZRa)
08a: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEa)
08b: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOE... (PEEb)
09a: IRON/SULFUR CLUSTER (SF4a)
10a: COENZYME Q10, (2Z,6E,10Z,14E,18E,2... (UQa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3NP
1
Ligand/Ion
3-NITROPROPANOIC ACID
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
GOL
1
Ligand/Ion
GLYCEROL
6
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
JZR
1
Ligand/Ion
HEXYL BETA-D-GLUCOPYRANOSIDE
8
PEE
2
Ligand/Ion
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
9
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
10
UQ
1
Ligand/Ion
COENZYME Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER
[
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]
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
LYS C:31 , TRP C:32 , SER C:33 , LEU C:34 , PRO C:35 , GLU C:120 , HOH C:1357 , TYR D:88 , TYR D:89
BINDING SITE FOR RESIDUE JZR C 142
02
AC2
SOFTWARE
GLY A:25 , ALA A:26 , GLY A:27 , GLY A:28 , ALA A:29 , VAL A:47 , THR A:48 , LYS A:49 , LEU A:50 , SER A:55 , HIS A:56 , THR A:57 , ALA A:59 , ALA A:60 , GLN A:61 , GLY A:62 , GLY A:63 , TYR A:176 , PHE A:177 , ALA A:178 , ALA A:212 , THR A:213 , GLY A:214 , THR A:224 , ASP A:232 , LEU A:263 , HIS A:364 , TYR A:365 , GLY A:396 , GLU A:397 , ARG A:408 , ALA A:411 , ASN A:412 , SER A:413 , LEU A:414 , LEU A:417 , 3NP A:1002 , HOH A:1008 , HOH A:1022 , HOH A:1045 , HOH A:1048 , HOH A:1063 , HOH B:1022
BINDING SITE FOR RESIDUE FAD A 1001
03
AC3
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 1002
04
AC4
SOFTWARE
CYS B:158 , ILE B:159 , CYS B:161 , ALA B:162 , CYS B:164 , MET B:185 , CYS B:225 , PRO B:226
BINDING SITE FOR RESIDUE SF4 B 1003
05
AC5
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
BINDING SITE FOR RESIDUE F3S B 1004
06
AC6
SOFTWARE
HIS B:216 , HIS C:42 , ARG C:43 , GLY C:46 , VAL C:47 , LEU C:49 , SER C:50 , HIS C:98 , HIS C:105 , HOH C:1509 , HOH C:1522 , HOH C:1525 , LEU D:20 , HIS D:46 , GLY D:50 , HOH D:1098
BINDING SITE FOR RESIDUE HEM C 143
07
AC7
SOFTWARE
GLY A:62 , PHE A:130 , HIS A:253 , THR A:265 , GLU A:266 , ARG A:297 , HIS A:364 , ARG A:408 , FAD A:1001
BINDING SITE FOR RESIDUE 3NP A 1002
08
AC8
SOFTWARE
PRO B:169 , TRP B:173 , ILE B:218 , ILE C:27 , TRP C:32 , MET C:36 , SER C:39 , ILE C:40 , ARG C:43 , HOH C:1006 , TYR D:58
BINDING SITE FOR RESIDUE UQ C 144
09
AC9
SOFTWARE
LEU D:24 , ALA D:27 , TYR D:28 , LEU D:39 , VAL D:97 , TRP D:101 , HOH D:1363
BINDING SITE FOR RESIDUE PEE D 104
10
BC1
SOFTWARE
LEU C:95 , TRP C:100 , ALA D:18 , GLY D:22
BINDING SITE FOR RESIDUE PEE C 145
11
BC2
SOFTWARE
ILE B:11 , LYS B:13 , LEU B:93
BINDING SITE FOR RESIDUE GOL B 1005
[
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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
(5, 5)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:12-105)
2: FRD_SDH_FAD_BINDING (A:54-63)
3: 2FE2S_FER_1 (B:65-73)
4: 4FE4S_FER_2 (B:148-178)
5: 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_CHICK
50-143
1
B:12-105
2
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_CHICK
98-107
1
A:54-63
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
SDHB_CHICK
103-111
1
B:65-73
4
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_CHICK
186-216
1
B:148-178
5
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_CHICK
196-207
1
B:158-169
[
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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
(3, 4)
Info
All SCOP Domains
1a: SCOP_d1yq4b2 (B:115-247)
2a: SCOP_d1yq4b1 (B:6-114)
3a: SCOP_d1yq4c_ (C:)
3b: SCOP_d1yq4d_ (D:)
View:
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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
:
Succinate dehydogenase
(16)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
1a
d1yq4b2
B:115-247
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)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
2a
d1yq4b1
B:6-114
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
:
automated matches
(11)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
3a
d1yq4c_
C:
3b
d1yq4d_
D:
[
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]
CATH Domains
(7, 8)
Info
all CATH domains
1a: CATH_1yq4A01 (A:8-256,A:361-439)
2a: CATH_1yq4B01 (B:6-114)
3a: CATH_1yq4A04 (A:557-621)
4a: CATH_1yq4B02 (B:115-247)
5a: CATH_1yq4C02 (C:33-141)
5b: CATH_1yq4D00 (D:2-103)
6a: CATH_1yq4A03 (A:440-556)
7a: CATH_1yq4C01 (C:2-32)
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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)
Chicken (Gallus gallus)
(6)
1a
1yq4A01
A:8-256,A:361-439
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Chicken (Gallus gallus)
(6)
2a
1yq4B01
B:6-114
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
succinate dehydrogenase protein domain
(23)
Chicken (Gallus gallus)
(6)
3a
1yq4A04
A:557-621
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)
Chicken (Gallus gallus)
(6)
4a
1yq4B02
B:115-247
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)
Chicken (Gallus gallus)
(6)
5a
1yq4C02
C:33-141
5b
1yq4D00
D:2-103
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.100, no name defined]
(37)
Chicken (Gallus gallus)
(6)
6a
1yq4A03
A:440-556
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(17)
Chicken (Gallus gallus)
(8)
7a
1yq4C01
C:2-32
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_CybS_1yq4D01 (D:2-102)
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(
)
Clan
:
FumRed-TM
(17)
Family
:
CybS
(3)
Gallus gallus (Chicken)
(2)
1a
CybS-1yq4D01
D:2-102
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