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1QLB
Asym. Unit
Info
Asym.Unit (394 KB)
Biol.Unit 1 (382 KB)
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(1)
Title
:
RESPIRATORY COMPLEX II-LIKE FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES
Authors
:
C. R. D. Lancaster, A. Kroeger, M. Auer, H. Michel
Date
:
25 Aug 99 (Deposition) - 29 Nov 99 (Release) - 18 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.33
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Oxidoreductase, Citric Acid Cycle, Respiratory Chain Iron-Sulphur Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. R. D. Lancaster, A. Kroeger, M. Auer, H. Michel
Structure Of Fumarate Reductase From Wolinella Succinogenes At 2. 2 Angstroms Resolution
Nature V. 402 377 1999
[
close entry info
]
Hetero Components
(8, 18)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
5a: FUMARIC ACID (FUMa)
5b: FUMARIC ACID (FUMb)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
6d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
7a: DODECYL-BETA-D-MALTOSIDE (LMTa)
7b: DODECYL-BETA-D-MALTOSIDE (LMTb)
8a: IRON/SULFUR CLUSTER (SF4a)
8b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
FUM
2
Ligand/Ion
FUMARIC ACID
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
LMT
2
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
8
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN C:30 , SER C:31 , GLY C:34 , LEU C:37 , PHE C:90 , HIS C:93 , ALA C:94 , ALA C:97 , LYS C:100 , PHE C:101 , TRP C:126 , GLY C:133 , MET C:136 , HIS C:182 , GLY C:183 , GLY C:186 , LEU C:190 , LYS C:193 , HOH C:2022 , HOH C:2023
BINDING SITE FOR RESIDUE HEM C1255
02
AC2
SOFTWARE
PHE C:40 , MET C:41 , HIS C:44 , ALA C:83 , VAL C:86 , HIS C:143 , LEU C:144 , MET C:147 , ILE C:154 , SER C:159 , ARG C:162 , TYR C:172 , LEU C:176 , GLY C:224 , PHE C:228
BINDING SITE FOR RESIDUE HEM C1256
03
AC3
SOFTWARE
VAL B:56 , CYS B:57 , ARG B:58 , GLY B:60 , ILE B:61 , CYS B:62 , GLY B:63 , CYS B:65 , CYS B:77
BINDING SITE FOR RESIDUE FES B1240
04
AC4
SOFTWARE
CYS B:161 , THR B:163 , ALA B:173 , CYS B:208 , MET B:209 , THR B:210 , LEU B:211 , LEU B:212 , ALA B:213 , CYS B:214
BINDING SITE FOR RESIDUE F3S B1241
05
AC5
SOFTWARE
CYS B:151 , ILE B:152 , GLU B:153 , CYS B:154 , GLY B:155 , CYS B:157 , CYS B:218 , PRO B:219
BINDING SITE FOR RESIDUE SF4 B1242
06
AC6
SOFTWARE
GLY A:12 , GLY A:13 , GLY A:14 , LEU A:15 , ALA A:16 , SER A:35 , LEU A:36 , ILE A:37 , SER A:42 , HIS A:43 , SER A:44 , ALA A:47 , GLY A:49 , GLY A:50 , LYS A:179 , ALA A:181 , ALA A:215 , THR A:216 , GLY A:217 , THR A:227 , ASN A:228 , THR A:235 , HIS A:369 , TYR A:370 , GLU A:393 , ARG A:404 , GLY A:407 , ASN A:408 , SER A:409 , VAL A:410 , FUM A:1657 , HOH A:2103 , HOH A:2147 , HOH A:2148 , HOH A:2149
BINDING SITE FOR RESIDUE FAD A1656
07
AC7
SOFTWARE
PHE A:141 , HIS A:257 , LEU A:267 , THR A:269 , ARG A:301 , HIS A:369 , ARG A:404 , GLY A:407 , FAD A:1656 , HOH A:2012 , HOH A:2094
BINDING SITE FOR RESIDUE FUM A1657
08
AC8
SOFTWARE
PRO C:102 , ASN C:104 , TYR C:108 , TRP C:127 , MET C:131 , PHE F:95 , MET F:98 , ARG F:99
BINDING SITE FOR RESIDUE LMT C1257
09
AC9
SOFTWARE
SER A:371 , MET A:372 , GLY A:373 , GLU A:393 , ALA A:395 , HOH A:2105
BINDING SITE FOR RESIDUE CA A1658
10
BC1
SOFTWARE
HOH E:2083 , GLN F:30 , SER F:31 , GLY F:34 , LEU F:37 , PHE F:90 , HIS F:93 , ALA F:94 , ALA F:97 , LYS F:100 , PHE F:101 , TRP F:126 , GLY F:133 , MET F:136 , HIS F:182 , GLY F:183 , GLY F:186 , LEU F:190 , LYS F:193 , HOH F:2022
BINDING SITE FOR RESIDUE HEM F1255
11
BC2
SOFTWARE
PHE F:40 , MET F:41 , HIS F:44 , ALA F:83 , VAL F:86 , HIS F:143 , LEU F:144 , MET F:147 , ILE F:154 , SER F:159 , ARG F:162 , TYR F:172 , LEU F:176 , GLY F:224 , PHE F:228
BINDING SITE FOR RESIDUE HEM F1256
12
BC3
SOFTWARE
VAL E:56 , CYS E:57 , ARG E:58 , GLY E:60 , ILE E:61 , CYS E:62 , GLY E:63 , CYS E:65 , CYS E:77
BINDING SITE FOR RESIDUE FES E1240
13
BC4
SOFTWARE
CYS E:161 , THR E:163 , ALA E:173 , CYS E:208 , MET E:209 , THR E:210 , LEU E:211 , LEU E:212 , ALA E:213 , CYS E:214
BINDING SITE FOR RESIDUE F3S E1241
14
BC5
SOFTWARE
CYS E:151 , ILE E:152 , GLU E:153 , CYS E:154 , GLY E:155 , CYS E:157 , CYS E:218 , PRO E:219
BINDING SITE FOR RESIDUE SF4 E1242
15
BC6
SOFTWARE
GLY D:12 , GLY D:13 , GLY D:14 , LEU D:15 , ALA D:16 , SER D:35 , LEU D:36 , ILE D:37 , SER D:42 , HIS D:43 , SER D:44 , ALA D:47 , GLY D:49 , GLY D:50 , LYS D:179 , ALA D:181 , ALA D:215 , THR D:216 , GLY D:217 , THR D:227 , ASN D:228 , THR D:235 , HIS D:369 , TYR D:370 , GLU D:393 , ARG D:404 , GLY D:407 , ASN D:408 , SER D:409 , VAL D:410 , FUM D:1657 , HOH D:2103 , HOH D:2146 , HOH D:2147 , HOH D:2148
BINDING SITE FOR RESIDUE FAD D1656
16
BC7
SOFTWARE
PHE D:141 , HIS D:257 , LEU D:267 , THR D:269 , ARG D:301 , HIS D:369 , ARG D:404 , GLY D:407 , FAD D:1656 , HOH D:2013 , HOH D:2108
BINDING SITE FOR RESIDUE FUM D1657
17
BC8
SOFTWARE
PHE C:95 , MET C:98 , ARG C:99 , PRO F:102 , ASN F:104 , TYR F:108 , TRP F:127 , MET F:131
BINDING SITE FOR RESIDUE LMT F1257
18
BC9
SOFTWARE
SER D:371 , MET D:372 , GLY D:373 , GLU D:393 , ALA D:395 , HOH D:2094
BINDING SITE FOR RESIDUE CA D1658
[
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:5-95,E:5-95)
2: FRD_SDH_FAD_BINDING (A:41-50,D:41-50)
3: 2FE2S_FER_1 (B:57-65,E:57-65)
4: 4FE4S_FER_2 (B:142-171,E:142-171)
5: 4FE4S_FER_1 (B:151-162,E:151-162)
;
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_WOLSU
5-95
2
B:5-95
E:5-95
2
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
FRDA_WOLSU
41-50
2
A:41-50
D:41-50
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
FRDB_WOLSU
57-65
2
B:57-65
E:57-65
4
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
FRDB_WOLSU
142-171
2
B:142-171
E:142-171
5
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
FRDB_WOLSU
151-162
2
B:151-162
E:151-162
[
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
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1qlbb1 (B:107-239)
1b: SCOP_d1qlbe1 (E:107-239)
2a: SCOP_d1qlba1 (A:458-655)
2b: SCOP_d1qlbd1 (D:458-655)
3a: SCOP_d1qlbb2 (B:1-106)
3b: SCOP_d1qlbe2 (E:1-106)
4a: SCOP_d1qlba3 (A:251-371)
4b: SCOP_d1qlbd3 (D:251-371)
5a: SCOP_d1qlba2 (A:1-250,A:372-457)
5b: SCOP_d1qlbd2 (D:1-250,D:372-457)
6a: SCOP_d1qlbc_ (C:)
6b: SCOP_d1qlbf_ (F:)
View:
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Classes
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Folds
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(
)
Superfamilies
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(
)
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)
Wolinella succinogenes [TaxId: 844]
(4)
1a
d1qlbb1
B:107-239
1b
d1qlbe1
E:107-239
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)
Wolinella succinogenes [TaxId: 844]
(5)
2a
d1qlba1
A:458-655
2b
d1qlbd1
D:458-655
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)
Wolinella succinogenes [TaxId: 844]
(4)
3a
d1qlbb2
B:1-106
3b
d1qlbe2
E: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
:
Fumarate reductase
(10)
Wolinella succinogenes [TaxId: 844]
(5)
4a
d1qlba3
A:251-371
4b
d1qlbd3
D:251-371
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)
Wolinella succinogenes [TaxId: 844]
(5)
5a
d1qlba2
A:1-250,A:372-457
5b
d1qlbd2
D:1-250,D:372-457
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
:
Fumarate reductase respiratory complex cytochrome b subunit, FrdC
(7)
Protein domain
:
Fumarate reductase respiratory complex cytochrome b subunit, FrdC
(4)
Wolinella succinogenes [TaxId: 844]
(4)
6a
d1qlbc_
C:
6b
d1qlbf_
F:
[
close SCOP info
]
CATH Domains
(6, 12)
Info
all CATH domains
1a: CATH_1qlbA01 (A:1-258,A:366-436)
1b: CATH_1qlbD01 (D:1-258,D:366-436)
2a: CATH_1qlbA02 (A:259-365)
2b: CATH_1qlbD02 (D:259-365)
3a: CATH_1qlbB01 (B:1-106)
3b: CATH_1qlbE01 (E:1-106)
4a: CATH_1qlbB02 (B:107-125,B:137-239)
4b: CATH_1qlbE02 (E:107-125,E:137-239)
5a: CATH_1qlbC00 (C:1-254)
5b: CATH_1qlbF00 (F:1-254)
6a: CATH_1qlbA03 (A:437-554)
6b: CATH_1qlbD03 (D:437-554)
View:
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Architectures
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Topologies
(
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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)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
1a
1qlbA01
A:1-258,A:366-436
1b
1qlbD01
D:1-258,D:366-436
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Flavocytochrome C3; Chain A, domain 1
(40)
Homologous Superfamily
:
Flavocytochrome C3; Chain A, domain 1
(40)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
2a
1qlbA02
A:259-365
2b
1qlbD02
D:259-365
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
3a
1qlbB01
B:1-106
3b
1qlbE01
E:1-106
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)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
4a
1qlbB02
B:107-125,B:137-239
4b
1qlbE02
E:107-125,E:137-239
Architecture
:
Up-down Bundle
(3216)
Topology
:
Fumarate Reductase Cytochrome B subunit
(17)
Homologous Superfamily
:
FUMARATE REDUCTASE CYTOCHROME B SUBUNIT;
(5)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
5a
1qlbC00
C:1-254
5b
1qlbF00
F:1-254
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.100, no name defined]
(37)
Wolinella succinogenes. Organism_taxid: 844. Wolinella succinogenes. Organism_taxid: 844.
(5)
6a
1qlbA03
A:437-554
6b
1qlbD03
D:437-554
[
close CATH info
]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_Fer4_8_1qlbE01 (E:147-222)
1b: PFAM_Fer4_8_1qlbE02 (E:147-222)
2a: PFAM_Fer2_3_1qlbE03 (E:6-112)
2b: PFAM_Fer2_3_1qlbE04 (E:6-112)
3a: PFAM_Sdh_cyt_1qlbF01 (F:105-226)
3b: PFAM_Sdh_cyt_1qlbF02 (F:105-226)
4a: PFAM_FAD_binding_2_1qlbD01 (D:7-410)
4b: PFAM_FAD_binding_2_1qlbD02 (D:7-410)
5a: PFAM_Succ_DH_flav_C_1qlbD03 (D:467-597)
5b: PFAM_Succ_DH_flav_C_1qlbD04 (D:467-597)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
4Fe-4S
(51)
Family
:
Fer4_8
(6)
Wolinella succinogenes
(1)
1a
Fer4_8-1qlbE01
E:147-222
1b
Fer4_8-1qlbE02
E:147-222
Clan
:
Fer2
(69)
Family
:
Fer2_3
(6)
Wolinella succinogenes
(1)
2a
Fer2_3-1qlbE03
E:6-112
2b
Fer2_3-1qlbE04
E:6-112
Clan
:
FumRed-TM
(17)
Family
:
Sdh_cyt
(10)
Wolinella succinogenes
(1)
3a
Sdh_cyt-1qlbF01
F:105-226
3b
Sdh_cyt-1qlbF02
F:105-226
Clan
:
NADP_Rossmann
(1239)
Family
:
FAD_binding_2
(21)
Wolinella succinogenes
(1)
4a
FAD_binding_2-1qlbD01
D:7-410
4b
FAD_binding_2-1qlbD02
D:7-410
Clan
:
no clan defined [family: Succ_DH_flav_C]
(11)
Family
:
Succ_DH_flav_C
(11)
Wolinella succinogenes
(1)
5a
Succ_DH_flav_C-1qlbD03
D:467-597
5b
Succ_DH_flav_C-1qlbD04
D:467-597
[
close Pfam info
]
Atom Selection
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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show bonds with a radius of 100 units (=0.4Å)
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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (394 KB)
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