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1KQF
Asym. Unit
Info
Asym.Unit (292 KB)
Biol.Unit 1 (832 KB)
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(1)
Title
:
FORMATE DEHYDROGENASE N FROM E. COLI
Authors
:
M. Jormakka, S. Tornroth, B. Byrne, S. Iwata
Date
:
05 Jan 02 (Deposition) - 15 Mar 02 (Release) - 06 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (3x)
Keywords
:
Oxidoreductase, Selenium, Selenocysteine, Secys, Molybdenum, Molybdopterin, Mpt, Molybdopterin Guanine Dinucleotide, Mgd, Iron Sulfur Cluster, Fe4S4, Formate, Dehydrogenase, Anaerobic, Integral Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Jormakka, S. Tornroth, B. Byrne, S. Iwata
Molecular Basis Of Proton Motive Force Generation: Structur Of Formate Dehydrogenase-N.
Science V. 295 1863 2002
[
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: MOLYBDENUM(VI) ION (6MOa)
2a: CARDIOLIPIN (CDLa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
4b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
5a: (SECa)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6MO
1
Ligand/Ion
MOLYBDENUM(VI) ION
2
CDL
1
Ligand/Ion
CARDIOLIPIN
3
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
5
SEC
1
Mod. Amino Acid
6
SF4
5
Ligand/Ion
IRON/SULFUR CLUSTER
[
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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
SEC A:196 , MGD A:1018 , MGD A:1019 , HOH A:1052
BINDING SITE FOR RESIDUE 6MO A 1016
02
AC2
SOFTWARE
CYS A:50 , TYR A:52 , CYS A:53 , GLY A:56 , CYS A:57 , CYS A:92 , LYS A:94 , GLY A:95 , VAL A:239
BINDING SITE FOR RESIDUE SF4 A 1017
03
AC3
SOFTWARE
CYS B:39 , ILE B:40 , GLY B:41 , CYS B:42 , LYS B:43 , CYS B:45 , MET B:80 , CYS B:179 , ILE B:184
BINDING SITE FOR RESIDUE SF4 B 805
04
AC4
SOFTWARE
LYS B:32 , CYS B:49 , ASN B:53 , THR B:78 , LYS B:97 , CYS B:160 , THR B:161 , LEU B:162 , CYS B:163 , PRO B:173 , CYS B:175
BINDING SITE FOR RESIDUE SF4 B 806
05
AC5
SOFTWARE
CYS B:100 , MET B:101 , CYS B:103 , GLY B:107 , CYS B:108 , CYS B:143 , PRO B:144 , LYS B:159
BINDING SITE FOR RESIDUE SF4 B 807
06
AC6
SOFTWARE
CYS B:112 , PRO B:113 , SER B:114 , ILE B:118 , CYS B:133 , ILE B:134 , CYS B:136 , GLY B:137 , CYS B:139 , VAL B:157
BINDING SITE FOR RESIDUE SF4 B 808
07
AC7
SOFTWARE
TYR A:101 , GLN A:192 , SEC A:196 , LEU A:410 , GLN A:414 , HIS A:448 , GLY A:556 , PHE A:557 , ASN A:558 , SER A:562 , ILE A:582 , ASP A:583 , PRO A:584 , LEU A:585 , THR A:587 , SER A:616 , THR A:617 , ASP A:649 , THR A:894 , ARG A:896 , HIS A:902 , THR A:903 , TRP A:904 , ASN A:989 , TYR A:1005 , LYS A:1006 , 6MO A:1016 , MGD A:1019 , HOH A:1029 , HOH A:1032 , HOH A:1041 , HOH A:1145 , HOH A:1147 , HOH A:1172 , HOH A:1174 , HOH A:1263
BINDING SITE FOR RESIDUE MGD A 1018
08
AC8
SOFTWARE
LYS A:94 , SEC A:196 , GLY A:230 , GLY A:231 , ASN A:232 , GLU A:235 , ALA A:236 , ASP A:259 , PRO A:260 , ARG A:261 , THR A:263 , SER A:277 , GLY A:278 , ASP A:280 , ALA A:409 , LEU A:410 , GLY A:411 , HIS A:415 , GLY A:447 , HIS A:448 , THR A:893 , TYR A:895 , ARG A:896 , LEU A:897 , THR A:898 , HIS A:900 , PHE A:901 , HIS A:902 , HIS A:975 , LYS A:1006 , 6MO A:1016 , MGD A:1018 , HOH A:1031 , HOH A:1046 , HOH A:1085 , HOH A:1138
BINDING SITE FOR RESIDUE MGD A 1019
09
AC9
SOFTWARE
TYR B:138 , TRP B:253 , PHE C:25 , VAL C:28 , ALA C:29 , GLY C:32 , PHE C:35 , PHE C:36 , ARG C:54 , HIS C:57 , PRO C:58 , GLY C:61 , ILE C:62 , ILE C:124 , LEU C:127 , LEU C:128 , GLY C:131 , ILE C:134 , HIS C:155 , ALA C:156 , HOH C:436 , HOH C:446 , HOH C:561
BINDING SITE FOR RESIDUE HEM C 809
10
BC1
SOFTWARE
ARG C:9 , HIS C:18 , TRP C:19 , VAL C:21 , VAL C:22 , PHE C:25 , PHE C:75 , ASN C:79 , TYR C:109 , GLN C:113 , ILE C:166 , HIS C:169 , MET C:170 , SER C:179 , MET C:183 , HOH C:1294 , HOH C:1729
BINDING SITE FOR RESIDUE HEM C 810
11
BC2
SOFTWARE
ASN B:15 , SER B:16 , ILE B:17 , PRO B:259 , ALA B:262 , ILE B:266 , HOH B:960 , PHE C:37 , PRO C:38 , THR C:39 , PHE C:47 , MET C:170 , HOH C:1083 , HOH C:1150 , HOH C:1263
BINDING SITE FOR RESIDUE CDL C 812
[
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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, 8)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (B:30-58|B:124-153|B:91-123|B:158-1...)
2: 4FE4S_MOW_BIS_MGD (A:43-106)
3: MOLYBDOPTERIN_PROK_1 (A:48-66)
4: 4FE4S_FER_1 (B:133-144)
5: MOLYBDOPTERIN_PROK_3 (A:927-954)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
FDNH_ECOLI
30-58
124-153
91-123
158-189
4
B:30-58
B:124-153
B:91-123
B:158-189
2
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
FDNG_ECOLI
43-106
1
A:43-106
3
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
FDNG_ECOLI
48-66
1
A:48-66
4
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
FDNH_ECOLI
133-144
1
B:133-144
5
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
FDNG_ECOLI
927-954
1
A:927-954
[
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]
Exons
(0, 0)
Info
All Exons
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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
(5, 5)
Info
All SCOP Domains
1a: SCOP_d1kqfa1 (A:851-1015)
2a: SCOP_d1kqfb1 (B:2-245)
3a: SCOP_d1kqfa2 (A:34-850)
4a: SCOP_d1kqfc_ (C:)
5a: SCOP_d1kqfb2 (B:246-290)
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Classes
(
)
(
)
Folds
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Formate dehydrogenase N, alpha subunit
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1kqfa1
A:851-1015
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Formate dehydrogenase N, iron-sulfur (beta) subunit
(2)
Escherichia coli [TaxId: 562]
(2)
2a
d1kqfb1
B:2-245
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Formate dehydrogenase N, alpha subunit
(2)
Escherichia coli [TaxId: 562]
(2)
3a
d1kqfa2
A:34-850
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Transmembrane di-heme cytochromes
(48)
Family
:
Formate dehydrogenase N, cytochrome (gamma) subunit
(2)
Protein domain
:
Formate dehydrogenase N, cytochrome (gamma) subunit
(2)
Escherichia coli [TaxId: 562]
(2)
4a
d1kqfc_
C:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor
(2)
Family
:
Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor
(2)
Protein domain
:
Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor
(2)
Escherichia coli [TaxId: 562]
(2)
5a
d1kqfb2
B:246-290
[
close SCOP info
]
CATH Domains
(6, 7)
Info
all CATH domains
1a: CATH_1kqfB01 (B:2-27,B:99-162)
1b: CATH_1kqfB02 (B:28-98,B:163-228)
2a: CATH_1kqfA03 (A:195-307,A:360-449,A:776-839)
3a: CATH_1kqfA02 (A:107-194,A:532-682)
4a: CATH_1kqfC00 (C:2-217)
5a: CATH_1kqfB03 (B:247-290)
6a: CATH_1kqfA04 (A:840-1015)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
1a
1kqfB01
B:2-27,B:99-162
1b
1kqfB02
B:28-98,B:163-228
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
2a
1kqfA03
A:195-307,A:360-449,A:776-839
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
3a
1kqfA02
A:107-194,A:532-682
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Fumarate Reductase Cytochrome B subunit
(17)
Homologous Superfamily
:
Transmembrane di-heme cytochromes, Chain C
(12)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
4a
1kqfC00
C:2-217
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(4)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
5a
1kqfB03
B:247-290
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Escherichia coli. Organism_taxid: 562. Strain: gl101. Escherichia coli. Organism_taxid: 562. Strain: gl101.
(2)
6a
1kqfA04
A:840-1015
[
close CATH info
]
Pfam Domains
(8, 8)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_1kqfC01 (C:7-186)
2a: PFAM_Fer4_10_1kqfB01 (B:92-144)
3a: PFAM_Fer4_11_1kqfB02 (B:91-189)
4a: PFAM_Fer4_4_1kqfB03 (B:36-56)
5a: PFAM_Molydop_binding_1kqfA01 (A:890-1009)
6a: PFAM_Form_deh_trans_1kqfB04 (B:246-290)
7a: PFAM_Molybdop_Fe4S4_1kqfA02 (A:43-104)
8a: PFAM_Molybdopterin_1kqfA03 (A:107-593)
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Clans
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N
(2)
Escherichia coli (strain K12)
(2)
1a
Cytochrom_B_N-1kqfC01
C:7-186
Clan
:
4Fe-4S
(51)
Family
:
Fer4_10
(4)
Escherichia coli (strain K12)
(2)
2a
Fer4_10-1kqfB01
B:92-144
Family
:
Fer4_11
(12)
Escherichia coli (strain K12)
(8)
3a
Fer4_11-1kqfB02
B:91-189
Family
:
Fer4_4
(2)
Escherichia coli (strain K12)
(2)
4a
Fer4_4-1kqfB03
B:36-56
Clan
:
AcetylDC-like
(37)
Family
:
Molydop_binding
(24)
Escherichia coli (strain K12)
(9)
5a
Molydop_binding-1kqfA01
A:890-1009
Clan
:
no clan defined [family: Form-deh_trans]
(2)
Family
:
Form-deh_trans
(2)
Escherichia coli (strain K12)
(2)
6a
Form-deh_trans-1kqfB04
B:246-290
Clan
:
no clan defined [family: Molybdop_Fe4S4]
(17)
Family
:
Molybdop_Fe4S4
(17)
Escherichia coli (strain K12)
(3)
7a
Molybdop_Fe4S4-1kqfA02
A:43-104
Clan
:
no clan defined [family: Molybdopterin]
(24)
Family
:
Molybdopterin
(24)
Escherichia coli (strain K12)
(9)
8a
Molybdopterin-1kqfA03
A:107-593
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