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1SIW
Biol. Unit 3
Info
Asym.Unit (343 KB)
Biol.Unit 1 (335 KB)
Biol.Unit 2 (659 KB)
Biol.Unit 3 (661 KB)
Biol.Unit 4 (660 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE APOMOLYBDO-NARGHI
Authors
:
R. A. Rothery, M. G. Bertero, R. Cammack, M. Palak, F. Blasco, N. C. Strynadka, J. H. Weiner
Date
:
01 Mar 04 (Deposition) - 08 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (2x)
Biol. Unit 3: A,B,C (2x)
Biol. Unit 4: A,B,C (2x)
Keywords
:
Apomolybdo-Narghi; Electron-Transfer; Membrane Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Rothery, M. G. Bertero, R. Cammack, M. Palak, F. Blasco, N. C. Strynadka, J. H. Weiner
The Catalytic Subunit Of Escherichia Coli Nitrate Reductase A Contains A Novel [4Fe-4S] Cluster With A High-Spin Ground State
Biochemistry V. 43 5324 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 22)
Info
All Hetero Components
1a: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE (3PHa)
1b: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE (3PHb)
2a: FE3-S4 CLUSTER (F3Sa)
3a: N-FORMYLMETHIONINE (FMEa)
4a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3PH
4
Ligand/Ion
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
2
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
3
FME
2
Mod. Amino Acid
N-FORMYLMETHIONINE
4
GDP
2
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
5
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
SF4
8
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:50 , TYR A:220 , ARG A:713 , SER A:714 , ASN A:715 , LEU A:716 , SER A:719 , SER A:720 , LEU A:771 , ASP A:772 , PHE A:773 , ARG A:774 , THR A:788 , TRP A:791 , LYS A:794 , ASP A:822 , ILE A:1097 , HIS A:1098 , SER A:1099 , THR A:1100 , HOH A:1597
BINDING SITE FOR RESIDUE GDP A 1247
02
AC2
SOFTWARE
ILE B:88 , TRP B:220 , ARG B:221 , SER C:39 , SER C:40 , GLN C:41 , MET C:48 , PHE C:55 , HIS C:56 , ILE C:59 , ARG C:112 , LEU C:130 , ARG C:202 , HIS C:205 , ILE C:206 , VAL C:209 , HOH C:809 , HOH C:812 , HOH C:815
BINDING SITE FOR RESIDUE HEM C 806
03
AC3
SOFTWARE
ILE C:59 , ILE C:62 , HIS C:66 , ALA C:90 , GLY C:94 , LEU C:133 , GLN C:136 , CYS C:137 , GLY C:140 , SER C:147 , MET C:156 , LEU C:159 , HIS C:187 , LEU C:188 , GLY C:191 , MET C:192 , PHE C:195 , HOH C:829
BINDING SITE FOR RESIDUE HEM C 807
04
AC4
SOFTWARE
HIS A:49 , GLY A:55 , SER A:56 , CYS A:57 , TRP A:59 , GLY A:91 , CYS A:92 , HOH A:1584 , HOH A:1633
BINDING SITE FOR RESIDUE SF4 A 1248
05
AC5
SOFTWARE
CYS B:16 , ILE B:17 , CYS B:19 , HIS B:20 , CYS B:22 , CYS B:263 , VAL B:264 , GLY B:265 , ILE B:267 , ARG B:268
BINDING SITE FOR RESIDUE SF4 B 802
06
AC6
SOFTWARE
CYS B:26 , TRP B:30 , ASN B:42 , CYS B:244 , ILE B:245 , PHE B:246 , CYS B:247 , THR B:257 , CYS B:259
BINDING SITE FOR RESIDUE SF4 B 803
07
AC7
SOFTWARE
CYS B:184 , GLU B:185 , CYS B:187 , PRO B:190 , ALA B:191 , CYS B:192 , CYS B:227 , TYR B:229 , ILE B:232 , LYS B:243
BINDING SITE FOR RESIDUE SF4 B 804
08
AC8
SOFTWARE
CYS B:196 , SER B:198 , ILE B:201 , CYS B:217 , ARG B:218 , GLY B:219 , TRP B:220 , ARG B:221 , MET B:222 , CYS B:223 , SER B:241
BINDING SITE FOR RESIDUE F3S B 805
09
AC9
SOFTWARE
PHE A:3 , ARG A:6 , HOH A:1620 , ARG B:218 , TRP C:25 , TYR C:28 , TRP C:207 , SER C:208
BINDING SITE FOR RESIDUE 3PH A 1309
10
BC1
SOFTWARE
HOH B:1453 , GLY C:124 , ALA C:125 , PHE C:200 , HOH C:824
BINDING SITE FOR RESIDUE 3PH B 1310
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(5, 14)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 ()
2: 4FE4S_MOW_BIS_MGD (A:42-106)
3: MOLYBDOPTERIN_PROK_1 (A:47-65)
4: MOLYBDOPTERIN_PROK_2 (A:776-793)
5: MOLYBDOPTERIN_PROK_3 (A:1124-1151)
;
View:
Select:
Label:
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.
NARH_ECOLI
7-35
175-206
208-237
6
B:7-35
B:175-206
B:208-237
2
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NARG_ECOLI
43-107
2
A:42-106
3
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
NARG_ECOLI
48-66
2
A:47-65
4
MOLYBDOPTERIN_PROK_2
PS00490
Prokaryotic molybdopterin oxidoreductases signature 2.
NARG_ECOLI
777-794
2
A:776-793
5
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
NARG_ECOLI
1125-1152
2
A:1124-1151
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1siwa1 (A:1075-1243)
2a: SCOP_d1siwb_ (B:)
3a: SCOP_d1siwa2 (A:1-1074)
4a: SCOP_d1siwc_ (C:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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
:
Respiratory nitrate reductase 1 alpha chain
(7)
Escherichia coli [TaxId: 562]
(7)
1a
d1siwa1
A:1075-1243
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
:
Respiratory nitrate reductase 1 beta chain
(11)
Escherichia coli [TaxId: 562]
(8)
2a
d1siwb_
B:
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
:
Respiratory nitrate reductase 1 alpha chain
(7)
Escherichia coli [TaxId: 562]
(7)
3a
d1siwa2
A:1-1074
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Respiratory nitrate reductase 1 gamma chain
(10)
Family
:
Respiratory nitrate reductase 1 gamma chain
(10)
Protein domain
:
Respiratory nitrate reductase 1 gamma chain
(6)
Escherichia coli [TaxId: 562]
(6)
4a
d1siwc_
C:
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1siwB01 (B:1-16,B:245-358,B:436-467)
2a: CATH_1siwB03 (B:359-435)
3a: CATH_1siwC01 (C:2-216)
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)
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)
(
)
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.
(6)
1a
1siwB01
B:1-16,B:245-358,B:436-467
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
nitrate reductase domain fold
(10)
Homologous Superfamily
:
nitrate reductase domain like
(10)
Escherichia coli. Organism_taxid: 562.
(6)
2a
1siwB03
B:359-435
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.
(6)
3a
1siwC01
C:2-216
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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