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1KF6
Asym. Unit
Info
Asym.Unit (357 KB)
Biol.Unit 1 (176 KB)
Biol.Unit 2 (179 KB)
Biol.Unit 3 (347 KB)
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(1)
Title
:
E. COLI QUINOL-FUMARATE REDUCTASE WITH BOUND INHIBITOR HQNO
Authors
:
T. M. Iverson, C. Luna-Chavez, L. R. Croal, G. Cecchini, D. C. Rees
Date
:
19 Nov 01 (Deposition) - 13 Mar 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: M,N,O,P (1x)
Biol. Unit 3: A,B,C,D,M,N,O,P (1x)
Keywords
:
Respiration, Fumarate Reductace, Succinate Dehydrogenase, Complex Ii, Quinol, Quinone, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. M. Iverson, C. Luna-Chavez, L. R. Croal, G. Cecchini, D. C. Rees
Crystallographic Studies Of The Escherichia Coli Quinol-Fumarate Reductase With Inhibitors Bound To The Quinol-Binding Site.
J. Biol. Chem. V. 277 16124 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(10, 23)
Info
All Hetero Components
01a: PENTAETHYLENE GLYCOL (1PEa)
02a: ACETATE ION (ACTa)
02b: ACETATE ION (ACTb)
02c: ACETATE ION (ACTc)
03a: O-DODECANYL OCTAETHYLENE GLYCOL (CE1a)
03b: O-DODECANYL OCTAETHYLENE GLYCOL (CE1b)
03c: O-DODECANYL OCTAETHYLENE GLYCOL (CE1c)
03d: O-DODECANYL OCTAETHYLENE GLYCOL (CE1d)
03e: O-DODECANYL OCTAETHYLENE GLYCOL (CE1e)
04a: FE3-S4 CLUSTER (F3Sa)
04b: FE3-S4 CLUSTER (F3Sb)
05a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
05b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
06a: FE2/S2 (INORGANIC) CLUSTER (FESa)
06b: FE2/S2 (INORGANIC) CLUSTER (FESb)
07a: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXI... (HQOa)
07b: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXI... (HQOb)
08a: POTASSIUM ION (Ka)
08b: POTASSIUM ION (Kb)
09a: OXALOACETATE ION (OAAa)
09b: OXALOACETATE ION (OAAb)
10a: IRON/SULFUR CLUSTER (SF4a)
10b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ACT
3
Ligand/Ion
ACETATE ION
3
CE1
5
Ligand/Ion
O-DODECANYL OCTAETHYLENE GLYCOL
4
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
5
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
7
HQO
2
Ligand/Ion
2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
8
K
2
Ligand/Ion
POTASSIUM ION
9
OAA
2
Ligand/Ion
OXALOACETATE ION
10
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(23, 23)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:357 , MET A:358 , GLY A:359 , GLU A:379 , SER A:381
BINDING SITE FOR RESIDUE K A 720
02
AC2
SOFTWARE
THR M:357 , MET M:358 , GLY M:359 , GLU M:379 , SER M:381
BINDING SITE FOR RESIDUE K M 820
03
AC3
SOFTWARE
HIS A:232 , LEU A:242 , THR A:244 , GLU A:245 , HIS A:355 , ARG A:390 , GLY A:392 , SER A:393 , FAD A:721
BINDING SITE FOR RESIDUE OAA A 702
04
AC4
SOFTWARE
ASP A:556 , ARG A:562 , GLU A:564
BINDING SITE FOR RESIDUE ACT A 703
05
AC5
SOFTWARE
ARG A:452 , GLY B:41 , ASP B:45
BINDING SITE FOR RESIDUE ACT B 704
06
AC6
SOFTWARE
PHE M:116 , HIS M:232 , LEU M:242 , THR M:244 , GLU M:245 , ARG M:287 , HIS M:355 , ARG M:390 , SER M:393 , FAD M:821
BINDING SITE FOR RESIDUE OAA M 802
07
AC7
SOFTWARE
TRP M:448 , ARG M:452 , GLY N:41 , ASP N:45 , TYR N:53 , TRP N:55
BINDING SITE FOR RESIDUE ACT N 803
08
AC8
SOFTWARE
SER B:56 , CYS B:57 , ARG B:58 , CYS B:62 , GLY B:63 , CYS B:65 , CYS B:77
BINDING SITE FOR RESIDUE FES B 244
09
AC9
SOFTWARE
CYS B:158 , GLN B:160 , CYS B:204 , THR B:205 , PHE B:206 , VAL B:207 , GLY B:208 , TYR B:209 , CYS B:210 , ILE B:224
BINDING SITE FOR RESIDUE F3S B 245
10
BC1
SOFTWARE
CYS B:148 , ILE B:149 , CYS B:151 , GLY B:152 , CYS B:154 , CYS B:214
BINDING SITE FOR RESIDUE SF4 B 246
11
BC2
SOFTWARE
GLY A:11 , ALA A:12 , GLY A:14 , ALA A:15 , SER A:36 , LYS A:37 , VAL A:38 , SER A:43 , HIS A:44 , THR A:45 , ALA A:48 , GLU A:49 , GLY A:50 , GLY A:51 , HIS A:155 , VAL A:157 , ALA A:191 , THR A:192 , GLY A:193 , THR A:203 , ASN A:204 , ASP A:211 , HIS A:355 , TYR A:356 , GLU A:379 , ARG A:390 , SER A:393 , ASN A:394 , SER A:395 , LEU A:396 , LEU A:399 , OAA A:702
BINDING SITE FOR RESIDUE FAD A 721
12
BC3
SOFTWARE
SER N:56 , CYS N:57 , ARG N:58 , CYS N:62 , GLY N:63 , CYS N:65 , CYS N:77
BINDING SITE FOR RESIDUE FES N 244
13
BC4
SOFTWARE
CYS N:158 , GLN N:160 , CYS N:204 , THR N:205 , PHE N:206 , VAL N:207 , GLY N:208 , CYS N:210 , ILE N:224
BINDING SITE FOR RESIDUE F3S N 245
14
BC5
SOFTWARE
CYS N:148 , ILE N:149 , ASN N:150 , CYS N:151 , GLY N:152 , CYS N:154 , CYS N:214 , VAL N:218
BINDING SITE FOR RESIDUE SF4 N 246
15
BC6
SOFTWARE
GLY M:11 , ALA M:12 , GLY M:13 , GLY M:14 , ALA M:15 , SER M:36 , LYS M:37 , VAL M:38 , SER M:43 , HIS M:44 , THR M:45 , ALA M:48 , GLU M:49 , GLY M:50 , GLY M:51 , HIS M:155 , PHE M:156 , VAL M:157 , ALA M:191 , THR M:192 , GLY M:193 , THR M:203 , ASN M:204 , ASP M:211 , LEU M:242 , HIS M:355 , TYR M:356 , GLY M:378 , GLU M:379 , ARG M:390 , SER M:393 , ASN M:394 , SER M:395 , LEU M:396 , LEU M:399 , OAA M:802
BINDING SITE FOR RESIDUE FAD M 821
16
BC7
SOFTWARE
THR B:205 , PHE B:206 , GLN B:225 , LYS B:228 , ARG C:28 , GLU C:29 , TRP D:14 , PHE D:17 , HIS D:80
BINDING SITE FOR RESIDUE HQO C 700
17
BC8
SOFTWARE
THR B:239 , TRP D:76 , ASP P:9 , LYS P:97 , TRP P:98 , TYR P:101 , GLY P:102 , CE1 P:810
BINDING SITE FOR RESIDUE CE1 P 710
18
BC9
SOFTWARE
ASP D:9 , TRP D:98 , ASP P:9 , PHE P:13 , TRP P:76 , CE1 P:710
BINDING SITE FOR RESIDUE CE1 P 810
19
CC1
SOFTWARE
TYR C:129 , LEU D:43 , PHE D:44 , PRO D:45 , GLY D:46 , LEU O:73 , CE1 O:813
BINDING SITE FOR RESIDUE CE1 O 811
20
CC2
SOFTWARE
VAL C:98 , PRO C:107 , SER C:111 , ALA C:114 , VAL C:118 , LEU O:124 , TYR O:129 , PRO P:45
BINDING SITE FOR RESIDUE CE1 O 812
21
CC3
SOFTWARE
TYR C:129 , ARG O:23 , PHE O:24 , GLY O:30 , CE1 O:811
BINDING SITE FOR RESIDUE CE1 O 813
22
CC4
SOFTWARE
GLY A:72 , ARG A:287 , ASP A:288 , LYS A:289 , GLN A:292 , TYR A:466 , GLN A:533
BINDING SITE FOR RESIDUE 1PE A 705
23
CC5
SOFTWARE
THR N:205 , PHE N:206 , GLN N:225 , LYS N:228 , ARG O:28 , GLU O:29 , TRP P:14 , PHE P:17 , ARG P:81
BINDING SITE FOR RESIDUE HQO N 800
[
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
(5, 10)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:15-96,N:15-96)
2: FRD_SDH_FAD_BINDING (A:42-51,M:42-51)
3: 2FE2S_FER_1 (B:57-65,N:57-65)
4: 4FE4S_FER_2 (B:139-168,N:139-168)
5: 4FE4S_FER_1 (B:148-159,N:148-159)
;
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.
FRDB_ECOLI
16-97
2
B:15-96
N:15-96
2
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
FRDA_ECOLI
43-52
2
A:42-51
M:42-51
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
FRDB_ECOLI
58-66
2
B:57-65
N:57-65
4
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
FRDB_ECOLI
140-169
2
B:139-168
N:139-168
5
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
FRDB_ECOLI
149-160
2
B:148-159
N:148-159
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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, 14)
Info
All SCOP Domains
1a: SCOP_d1kf6b1 (B:106-243)
1b: SCOP_d1kf6n1 (N:106-243)
2a: SCOP_d1kf6a1 (A:443-576)
2b: SCOP_d1kf6m1 (M:443-576)
3a: SCOP_d1kf6b2 (B:1-105)
3b: SCOP_d1kf6n2 (N:1-105)
4a: SCOP_d1kf6a3 (A:226-357)
4b: SCOP_d1kf6m3 (M:226-357)
5a: SCOP_d1kf6a2 (A:0-225,A:358-442)
5b: SCOP_d1kf6m2 (M:0-225,M:358-442)
6a: SCOP_d1kf6c_ (C:)
6b: SCOP_d1kf6o_ (O:)
7a: SCOP_d1kf6d_ (D:)
7b: SCOP_d1kf6p_ (P:)
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
:
Fumarate reductase
(11)
Escherichia coli [TaxId: 562]
(6)
1a
d1kf6b1
B:106-243
1b
d1kf6n1
N:106-243
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
:
Fumarate reductase
(10)
Escherichia coli [TaxId: 562]
(5)
2a
d1kf6a1
A:443-576
2b
d1kf6m1
M:443-576
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
:
Fumarate reductase iron-sulfur protein, N-terminal domain
(11)
Escherichia coli [TaxId: 562]
(6)
3a
d1kf6b2
B:1-105
3b
d1kf6n2
N:1-105
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
:
Fumarate reductase
(10)
Escherichia coli [TaxId: 562]
(5)
4a
d1kf6a3
A:226-357
4b
d1kf6m3
M:226-357
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
:
Fumarate reductase
(10)
Escherichia coli [TaxId: 562]
(5)
5a
d1kf6a2
A:0-225,A:358-442
5b
d1kf6m2
M:0-225,M:358-442
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
:
Fumarate reductase subunit FrdC
(7)
Escherichia coli [TaxId: 562]
(5)
6a
d1kf6c_
C:
6b
d1kf6o_
O:
Protein domain
:
Fumarate reductase subunit FrdD
(7)
Escherichia coli [TaxId: 562]
(6)
7a
d1kf6d_
D:
7b
d1kf6p_
P:
[
close SCOP info
]
CATH Domains
(7, 16)
Info
all CATH domains
1a: CATH_1kf6A01 (A:0-235,A:352-421)
1b: CATH_1kf6M01 (M:0-235,M:352-421)
2a: CATH_1kf6A02 (A:236-351)
2b: CATH_1kf6M02 (M:236-351)
3a: CATH_1kf6B01 (B:2-105)
3b: CATH_1kf6N01 (N:2-105)
4a: CATH_1kf6A04 (A:542-576)
4b: CATH_1kf6M04 (M:542-576)
5a: CATH_1kf6B02 (B:106-243)
5b: CATH_1kf6N02 (N:106-243)
6a: CATH_1kf6D00 (D:0-118)
6b: CATH_1kf6P00 (P:0-118)
6c: CATH_1kf6C00 (C:1-130)
6d: CATH_1kf6O00 (O:1-130)
7a: CATH_1kf6A03 (A:422-541)
7b: CATH_1kf6M03 (M:422-541)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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.
(12)
1a
1kf6A01
A:0-235,A:352-421
1b
1kf6M01
M:0-235,M:352-421
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.
(2)
2a
1kf6A02
A:236-351
2b
1kf6M02
M:236-351
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
1kf6B01
B:2-105
3b
1kf6N01
N:2-105
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)
4a
1kf6A04
A:542-576
4b
1kf6M04
M:542-576
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)
5a
1kf6B02
B:106-243
5b
1kf6N02
N:106-243
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)
6a
1kf6D00
D:0-118
6b
1kf6P00
P:0-118
6c
1kf6C00
C:1-130
6d
1kf6O00
O:1-130
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)
7a
1kf6A03
A:422-541
7b
1kf6M03
M:422-541
[
close CATH info
]
Pfam Domains
(6, 12)
Info
all PFAM domains
1a: PFAM_Fer4_8_1kf6N01 (N:144-218)
1b: PFAM_Fer4_8_1kf6N02 (N:144-218)
2a: PFAM_Fer2_3_1kf6N03 (N:7-111)
2b: PFAM_Fer2_3_1kf6N04 (N:7-111)
3a: PFAM_Fumarate_red_C_1kf6O01 (O:1-129)
3b: PFAM_Fumarate_red_C_1kf6O02 (O:1-129)
4a: PFAM_Fumarate_red_D_1kf6P01 (P:1-117)
4b: PFAM_Fumarate_red_D_1kf6P02 (P:1-117)
5a: PFAM_FAD_binding_2_1kf6M01 (M:6-396)
5b: PFAM_FAD_binding_2_1kf6M02 (M:6-396)
6a: PFAM_Succ_DH_flav_C_1kf6M03 (M:452-576)
6b: PFAM_Succ_DH_flav_C_1kf6M04 (M:452-576)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
4Fe-4S
(51)
Family
:
Fer4_8
(6)
Escherichia coli (strain K12)
(3)
1a
Fer4_8-1kf6N01
N:144-218
1b
Fer4_8-1kf6N02
N:144-218
Clan
:
Fer2
(69)
Family
:
Fer2_3
(6)
Escherichia coli (strain K12)
(3)
2a
Fer2_3-1kf6N03
N:7-111
2b
Fer2_3-1kf6N04
N:7-111
Clan
:
FumRed-TM
(17)
Family
:
Fumarate_red_C
(5)
Escherichia coli (strain K12)
(3)
3a
Fumarate_red_C-1kf6O01
O:1-129
3b
Fumarate_red_C-1kf6O02
O:1-129
Family
:
Fumarate_red_D
(5)
Escherichia coli (strain K12)
(3)
4a
Fumarate_red_D-1kf6P01
P:1-117
4b
Fumarate_red_D-1kf6P02
P:1-117
Clan
:
NADP_Rossmann
(1239)
Family
:
FAD_binding_2
(21)
Escherichia coli (strain K12)
(4)
5a
FAD_binding_2-1kf6M01
M:6-396
5b
FAD_binding_2-1kf6M02
M:6-396
Clan
:
no clan defined [family: Succ_DH_flav_C]
(11)
Family
:
Succ_DH_flav_C
(11)
Escherichia coli (strain K12)
(4)
6a
Succ_DH_flav_C-1kf6M03
M:452-576
6b
Succ_DH_flav_C-1kf6M04
M:452-576
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