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2WDR
Asym. Unit
Info
Asym.Unit (496 KB)
Biol.Unit 1 (166 KB)
Biol.Unit 2 (167 KB)
Biol.Unit 3 (167 KB)
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(1)
Title
:
E. COLI SUCCINATE:QUINONE OXIDOREDUCTASE (SQR) WITH PENTACHLOROPHENOL BOUND
Authors
:
J. Ruprecht, V. Yankovskaya, E. Maklashina, S. Iwata, G. Cecchini
Date
:
25 Mar 09 (Deposition) - 25 Aug 09 (Release) - 04 Feb 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Succinate Dehydrogenase Activity, Cell Inner Membrane, Tricarboxylic Acid Cycle, Cell Membrane, Metal-Binding, Transmembrane, Transport, Iron-Sulfur, Flavoprotein, Oxidoreductase, Electron Transport, Fad, Iron, Heme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Ruprecht, V. Yankovskaya, E. Maklashina, S. Iwata, G. Cecchini
Structure Of Escherichia Coli Succinate:Quinone Oxidoreductase With An Occupied And Empty Quinone- Binding Site.
J. Biol. Chem. V. 284 29836 2009
[
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Hetero Components
(8, 24)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
1c: FE3-S4 CLUSTER (F3Sc)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
6a: PENTACHLOROPHENOL (PCIa)
6b: PENTACHLOROPHENOL (PCIb)
6c: PENTACHLOROPHENOL (PCIc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
8a: MALATE LIKE INTERMEDIATE (TEOa)
8b: MALATE LIKE INTERMEDIATE (TEOb)
8c: MALATE LIKE INTERMEDIATE (TEOc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
3
Ligand/Ion
FE3-S4 CLUSTER
2
FAD
3
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
3
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
NA
3
Ligand/Ion
SODIUM ION
6
PCI
3
Ligand/Ion
PENTACHLOROPHENOL
7
SF4
3
Ligand/Ion
IRON/SULFUR CLUSTER
8
TEO
3
Ligand/Ion
MALATE LIKE INTERMEDIATE
[
close Hetero Component info
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Sites
(24, 24)
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)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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 , LEU A:252 , HIS A:354 , 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 , TEO A:1589
BINDING SITE FOR RESIDUE FAD A 601
02
AC2
SOFTWARE
SER B:54 , CYS B:55 , ARG B:56 , GLY B:58 , CYS B:60 , GLY B:61 , ASP B:63 , CYS B:75
BINDING SITE FOR RESIDUE FES B 302
03
AC3
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
04
AC4
SOFTWARE
CYS B:159 , PRO B:172 , CYS B:206 , HIS B:207 , SER B:208 , MET B:210 , ASN B:211 , CYS B:212 , THR B:223
BINDING SITE FOR RESIDUE F3S B 304
05
AC5
SOFTWARE
GLY E:14 , ALA E:15 , GLY E:16 , GLY E:17 , ALA E:18 , SER E:37 , LYS E:38 , VAL E:39 , SER E:44 , HIS E:45 , THR E:46 , SER E:48 , ALA E:49 , GLN E:50 , GLY E:51 , GLY E:52 , TRP E:164 , TYR E:165 , ALA E:166 , ALA E:201 , THR E:202 , GLY E:203 , ASN E:214 , ASP E:221 , LEU E:252 , HIS E:354 , TYR E:355 , GLY E:387 , GLU E:388 , ARG E:399 , GLY E:402 , ASN E:403 , SER E:404 , LEU E:405 , LEU E:408 , TEO E:1589
BINDING SITE FOR RESIDUE FAD E 601
06
AC6
SOFTWARE
SER F:54 , CYS F:55 , ARG F:56 , GLY F:58 , VAL F:59 , CYS F:60 , GLY F:61 , ASP F:63 , CYS F:75
BINDING SITE FOR RESIDUE FES F 302
07
AC7
SOFTWARE
CYS F:149 , ILE F:150 , CYS F:152 , ALA F:153 , CYS F:154 , CYS F:155 , CYS F:216 , PRO F:217
BINDING SITE FOR RESIDUE SF4 F 303
08
AC8
SOFTWARE
CYS F:159 , PRO F:172 , CYS F:206 , HIS F:207 , SER F:208 , MET F:210 , CYS F:212 , THR F:223
BINDING SITE FOR RESIDUE F3S F 304
09
AC9
SOFTWARE
GLY I:14 , ALA I:15 , GLY I:16 , GLY I:17 , ALA I:18 , SER I:37 , LYS I:38 , VAL I:39 , SER I:44 , HIS I:45 , THR I:46 , SER I:48 , ALA I:49 , GLN I:50 , GLY I:51 , GLY I:52 , TRP I:164 , TYR I:165 , ALA I:166 , ALA I:201 , THR I:202 , GLY I:203 , ASN I:214 , ASP I:221 , LEU I:252 , HIS I:354 , TYR I:355 , GLY I:387 , GLU I:388 , ARG I:399 , GLY I:402 , ASN I:403 , SER I:404 , LEU I:405 , LEU I:408 , TEO I:1589
BINDING SITE FOR RESIDUE FAD I 601
10
BC1
SOFTWARE
SER J:54 , CYS J:55 , ARG J:56 , GLY J:58 , VAL J:59 , CYS J:60 , GLY J:61 , ASP J:63 , CYS J:75
BINDING SITE FOR RESIDUE FES J 302
11
BC2
SOFTWARE
CYS J:149 , ILE J:150 , CYS J:152 , CYS J:154 , CYS J:155 , CYS J:216
BINDING SITE FOR RESIDUE SF4 J 303
12
BC3
SOFTWARE
CYS J:159 , CYS J:206 , HIS J:207 , SER J:208 , MET J:210 , CYS J:212 , THR J:223
BINDING SITE FOR RESIDUE F3S J 304
13
BC4
SOFTWARE
HIS C:30 , ARG C:31 , THR C:37 , PHE C:38 , HIS C:84 , VAL C:85 , GLY C:88 , HIS C:91 , ARG D:20 , LEU D:26 , THR D:27 , HIS D:71 , GLY D:75 , MET D:76 , GLN D:78
BINDING SITE FOR RESIDUE HEM C1130
14
BC5
SOFTWARE
PRO B:160 , TRP B:164 , ILE B:209 , PHE C:20 , ALA C:24 , SER C:27 , ILE C:28 , ARG C:31 , TYR D:83
BINDING SITE FOR RESIDUE PCI C1131
15
BC6
SOFTWARE
GLY A:51 , 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
BINDING SITE FOR RESIDUE TEO A1589
16
BC7
SOFTWARE
MET A:356 , MET A:357 , GLY A:358 , GLU A:388 , ALA A:390
BINDING SITE FOR RESIDUE NA A1590
17
BC8
SOFTWARE
HIS F:207 , HIS G:30 , ARG G:31 , GLY G:34 , THR G:37 , PHE G:38 , HIS G:84 , VAL G:85 , GLY G:88 , HIS G:91 , ARG H:20 , ALA H:23 , LEU H:26 , THR H:27 , HIS H:71 , GLY H:75 , GLN H:78
BINDING SITE FOR RESIDUE HEM G1130
18
BC9
SOFTWARE
PRO F:160 , TRP F:164 , LEU G:15 , PHE G:20 , ALA G:24 , SER G:27 , ILE G:28 , ARG G:31 , TYR H:83
BINDING SITE FOR RESIDUE PCI G1131
19
CC1
SOFTWARE
GLY E:51 , PHE E:119 , HIS E:242 , THR E:254 , GLU E:255 , ARG E:286 , HIS E:354 , ARG E:399 , GLY E:401 , GLY E:402 , FAD E:601
BINDING SITE FOR RESIDUE TEO E1589
20
CC2
SOFTWARE
MET E:356 , MET E:357 , GLY E:358 , GLU E:388 , ALA E:390
BINDING SITE FOR RESIDUE NA E1590
21
CC3
SOFTWARE
HIS J:207 , HIS K:30 , ARG K:31 , THR K:37 , HIS K:84 , VAL K:85 , GLY K:88 , ARG L:20 , LEU L:26 , THR L:27 , HIS L:71 , GLY L:75 , GLN L:78
BINDING SITE FOR RESIDUE HEM K1130
22
CC4
SOFTWARE
PRO J:160 , TRP J:164 , ILE J:209 , LEU K:15 , PHE K:20 , ALA K:24 , SER K:27 , ILE K:28 , ARG K:31 , TYR L:83
BINDING SITE FOR RESIDUE PCI K1131
23
CC5
SOFTWARE
GLY I:51 , PHE I:119 , HIS I:242 , LEU I:252 , THR I:254 , GLU I:255 , ARG I:286 , HIS I:354 , ARG I:399 , GLY I:401 , GLY I:402 , FAD I:601
BINDING SITE FOR RESIDUE TEO I1589
24
CC6
SOFTWARE
TYR I:355 , MET I:356 , MET I:357 , GLY I:358 , GLU I:388 , ALA I:390
BINDING SITE FOR RESIDUE NA I1590
[
close Site info
]
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
(6, 18)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:8-97,F:8-97,J:8-97)
2: SDH_CYT_1 (C:9-33,G:9-33,K:9-33)
3: FRD_SDH_FAD_BINDING (A:43-52,E:43-52,I:43-52)
4: SDH_CYT_2 (C:84-97,G:84-97,K:84-97)
5: 4FE4S_FER_2 (B:139-169,F:139-169,J:139-169)
6: 4FE4S_FER_1 (B:149-160,F:149-160,J:149-160)
;
View:
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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
3
B:8-97
F:8-97
J:8-97
2
SDH_CYT_1
PS01000
Succinate dehydrogenase cytochrome b subunit signature 1.
DHSC_ECOLI
9-33
3
C:9-33
G:9-33
K:9-33
3
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_ECOLI
43-52
3
A:43-52
E:43-52
I:43-52
4
SDH_CYT_2
PS01001
Succinate dehydrogenase cytochrome b subunit signature 2.
DHSC_ECOLI
84-97
3
C:84-97
G:84-97
K:84-97
5
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_ECOLI
139-169
3
B:139-169
F:139-169
J:139-169
6
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_ECOLI
149-160
3
B:149-160
F:149-160
J: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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
[
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CATH Domains
(6, 21)
Info
all CATH domains
1a: CATH_2wdrA01 (A:1-245,A:351-430)
1b: CATH_2wdrE01 (E:1-245,E:351-430)
1c: CATH_2wdrI01 (I:1-245,I:351-430)
2a: CATH_2wdrB01 (B:1-106)
2b: CATH_2wdrF01 (F:1-106)
2c: CATH_2wdrJ01 (J:1-106)
3a: CATH_2wdrA04 (A:548-588)
3b: CATH_2wdrE04 (E:548-588)
3c: CATH_2wdrI04 (I:548-588)
4a: CATH_2wdrB02 (B:107-238)
4b: CATH_2wdrF02 (F:107-238)
4c: CATH_2wdrJ02 (J:107-238)
5a: CATH_2wdrC00 (C:8-129)
5b: CATH_2wdrG00 (G:8-129)
5c: CATH_2wdrK00 (K:8-129)
5d: CATH_2wdrD00 (D:11-115)
5e: CATH_2wdrH00 (H:11-115)
5f: CATH_2wdrL00 (L:11-115)
6a: CATH_2wdrA03 (A:431-547)
6b: CATH_2wdrE03 (E:431-547)
6c: CATH_2wdrI03 (I: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
2wdrA01
A:1-245,A:351-430
1b
2wdrE01
E:1-245,E:351-430
1c
2wdrI01
I:1-245,I: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
2wdrB01
B:1-106
2b
2wdrF01
F:1-106
2c
2wdrJ01
J: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
2wdrA04
A:548-588
3b
2wdrE04
E:548-588
3c
2wdrI04
I: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
2wdrB02
B:107-238
4b
2wdrF02
F:107-238
4c
2wdrJ02
J: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
2wdrC00
C:8-129
5b
2wdrG00
G:8-129
5c
2wdrK00
K:8-129
5d
2wdrD00
D:11-115
5e
2wdrH00
H:11-115
5f
2wdrL00
L: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
2wdrA03
A:431-547
6b
2wdrE03
E:431-547
6c
2wdrI03
I:431-547
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Sdh_cyt_2wdrK01 (K:8-124)
1b: PFAM_Sdh_cyt_2wdrK02 (K:8-124)
1c: PFAM_Sdh_cyt_2wdrK03 (K:8-124)
1d: PFAM_Sdh_cyt_2wdrL01 (L:11-113)
1e: PFAM_Sdh_cyt_2wdrL02 (L:11-113)
1f: PFAM_Sdh_cyt_2wdrL03 (L:11-113)
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Clan
:
FumRed-TM
(17)
Family
:
Sdh_cyt
(10)
Escherichia coli (strain K12)
(8)
1a
Sdh_cyt-2wdrK01
K:8-124
1b
Sdh_cyt-2wdrK02
K:8-124
1c
Sdh_cyt-2wdrK03
K:8-124
1d
Sdh_cyt-2wdrL01
L:11-113
1e
Sdh_cyt-2wdrL02
L:11-113
1f
Sdh_cyt-2wdrL03
L:11-113
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