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1YCF
Biol. Unit 3
Info
Asym.Unit (267 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (133 KB)
Biol.Unit 3 (259 KB)
Biol.Unit 4 (133 KB)
Biol.Unit 5 (133 KB)
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(1)
Title
:
OXIDIZED (DI-FERRIC) FPRA FROM MOORELLA THERMOACETICA
Authors
:
R. Silaghi-Dumitrescu, D. M. Kurtz, W. N. Lanzilotta
Date
:
22 Dec 04 (Deposition) - 19 Apr 05 (Release) - 21 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: A,C (1x)
Biol. Unit 5: B,D (1x)
Keywords
:
Scavenging Nitric Oxide Reductase, Diron Site Structure, Diferrous- Dinitrosyl, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Silaghi-Dumitrescu, D. M. Kurtz Jr, L. G. Ljungdahl, W. N. Lanzilotta
X-Ray Crystal Structures Of Moorella Thermoacetica Fpra. Novel Diiron Site Structure And Mechanistic Insights Into A Scavenging Nitric Oxide Reductase.
Biochemistry V. 44 6492 2005
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: MU-OXO-DIIRON (FEOa)
1b: MU-OXO-DIIRON (FEOb)
1c: MU-OXO-DIIRON (FEOc)
1d: MU-OXO-DIIRON (FEOd)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: OXYGEN MOLECULE (OXYa)
3b: OXYGEN MOLECULE (OXYb)
3c: OXYGEN MOLECULE (OXYc)
3d: OXYGEN MOLECULE (OXYd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FEO
2
Ligand/Ion
MU-OXO-DIIRON
2
FMN
2
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
OXY
2
Ligand/Ion
OXYGEN MOLECULE
4
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:2 , GLU A:60 , HIS C:271 , ASP C:275
BINDING SITE FOR RESIDUE ZN A 502
02
AC2
SOFTWARE
HIS A:271 , ASP A:275 , SER C:2 , GLU C:60
BINDING SITE FOR RESIDUE ZN A 503
03
AC3
SOFTWARE
VAL B:17 , HIS D:271
BINDING SITE FOR RESIDUE ZN B 512
04
AC4
SOFTWARE
HIS A:81 , GLU A:83 , ASP A:85 , HIS A:86 , HIS A:148 , ASP A:167 , HIS A:228 , OXY A:501
BINDING SITE FOR RESIDUE FEO A 500
05
AC5
SOFTWARE
PHE A:24 , HIS A:25 , GLU A:83 , TYR A:195 , ILE A:199 , FEO A:500
BINDING SITE FOR RESIDUE OXY A 501
06
AC6
SOFTWARE
THR A:261 , MET A:262 , TRP A:263 , LEU A:264 , SER A:265 , THR A:266 , PRO A:312 , THR A:313 , ILE A:314 , ASN A:315 , ASN A:316 , TYR A:345 , GLY A:346 , TRP A:347 , GLY A:348 , GLY A:349 , TRP A:376 , HOH A:623 , HIS B:25 , GLU B:83 , TRP B:149
BINDING SITE FOR RESIDUE FMN A 701
07
AC7
SOFTWARE
HIS B:25 , HIS B:81 , GLU B:83 , ASP B:85 , HIS B:86 , HIS B:148 , ASP B:167 , HIS B:228 , OXY B:511
BINDING SITE FOR RESIDUE FEO B 510
08
AC8
SOFTWARE
PHE B:24 , HIS B:25 , ASP B:167 , TYR B:195 , HIS B:228 , FEO B:510
BINDING SITE FOR RESIDUE OXY B 511
09
AC9
SOFTWARE
HIS A:25 , GLU A:83 , TRP A:149 , THR B:261 , MET B:262 , TRP B:263 , LEU B:264 , SER B:265 , THR B:266 , PRO B:312 , THR B:313 , ILE B:314 , ASN B:315 , ASN B:316 , TYR B:345 , GLY B:346 , TRP B:347 , GLY B:348 , GLY B:349 , TRP B:376
BINDING SITE FOR RESIDUE FMN B 702
10
BC1
SOFTWARE
HIS C:81 , GLU C:83 , ASP C:85 , HIS C:86 , HIS C:148 , ASP C:167 , HIS C:228 , OXY C:521
BINDING SITE FOR RESIDUE FEO C 520
11
BC2
SOFTWARE
PHE C:24 , HIS C:25 , GLU C:83 , HIS C:148 , ASP C:167 , TYR C:195 , ILE C:199 , FEO C:520
BINDING SITE FOR RESIDUE OXY C 521
12
BC3
SOFTWARE
THR C:261 , MET C:262 , TRP C:263 , LEU C:264 , SER C:265 , THR C:266 , PRO C:312 , THR C:313 , ILE C:314 , ASN C:315 , ASN C:316 , ALA C:344 , TYR C:345 , GLY C:346 , TRP C:347 , GLY C:348 , GLY C:349 , TRP C:376 , HOH C:650 , HIS D:25 , GLU D:83 , TRP D:149
BINDING SITE FOR RESIDUE FMN C 703
13
BC4
SOFTWARE
HIS D:81 , GLU D:83 , ASP D:85 , HIS D:86 , HIS D:148 , ASP D:167 , HIS D:228 , OXY D:531
BINDING SITE FOR RESIDUE FEO D 530
14
BC5
SOFTWARE
PHE D:24 , HIS D:25 , GLU D:83 , HIS D:148 , ASP D:167 , TYR D:195 , HIS D:228 , FEO D:530
BINDING SITE FOR RESIDUE OXY D 531
15
BC6
SOFTWARE
HIS C:25 , GLU C:83 , TRP C:149 , THR D:261 , MET D:262 , TRP D:263 , LEU D:264 , SER D:265 , THR D:266 , PRO D:312 , THR D:313 , ASN D:315 , ASN D:316 , ALA D:344 , TYR D:345 , GLY D:346 , TRP D:347 , GLY D:348 , GLY D:349 , TRP D:376
BINDING SITE FOR RESIDUE FMN D 704
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FLAVODOXIN_LIKE (A:255-394,B:255-394,C:255-394,D:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FLAVODOXIN_LIKE
PS50902
Flavodoxin-like domain profile.
FPRA_MOOTA
255-394
4
A:255-394
B:255-394
C:255-394
D:255-394
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1ycfb2 (B:2-250)
1b: SCOP_d1ycfc2 (C:2-250)
1c: SCOP_d1ycfd2 (D:2-250)
2a: SCOP_d1ycfa2 (A:2-250)
3a: SCOP_d1ycfb1 (B:251-399)
3b: SCOP_d1ycfc1 (C:251-399)
3c: SCOP_d1ycfd1 (D:251-399)
4a: SCOP_d1ycfa1 (A:251-399)
View:
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Classes
(
)
(
)
Folds
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-hydrolase/oxidoreductase
(184)
Superfamily
:
Metallo-hydrolase/oxidoreductase
(184)
Family
:
ROO N-terminal domain-like
(9)
Protein domain
:
automated matches
(3)
Moorella thermoacetica [TaxId: 1525]
(1)
1a
d1ycfb2
B:2-250
1b
d1ycfc2
C:2-250
1c
d1ycfd2
D:2-250
Protein domain
:
Nitric oxide reductase N-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
2a
d1ycfa2
A:2-250
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Flavoproteins
(208)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Moorella thermoacetica [TaxId: 1525]
(1)
3a
d1ycfb1
B:251-399
3b
d1ycfc1
C:251-399
3c
d1ycfd1
D:251-399
Family
:
Flavodoxin-related
(81)
Protein domain
:
Nitric oxide reductase C-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
4a
d1ycfa1
A:251-399
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ycfA02 (A:254-396)
1b: CATH_1ycfB02 (B:254-396)
1c: CATH_1ycfC02 (C:254-396)
1d: CATH_1ycfD02 (D:254-396)
2a: CATH_1ycfA01 (A:2-248)
2b: CATH_1ycfB01 (B:2-248)
2c: CATH_1ycfC01 (C:2-248)
2d: CATH_1ycfD01 (D:2-248)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.360, no name defined]
(150)
Moorella thermoacetica. Organism_taxid: 1525.
(2)
1a
1ycfA02
A:254-396
1b
1ycfB02
B:254-396
1c
1ycfC02
C:254-396
1d
1ycfD02
D:254-396
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Metallo-beta-lactamase; Chain A
(92)
Homologous Superfamily
:
Metallo-beta-lactamase, chain A
(92)
Moorella thermoacetica. Organism_taxid: 1525.
(2)
2a
1ycfA01
A:2-248
2b
1ycfB01
B:2-248
2c
1ycfC01
C:2-248
2d
1ycfD01
D:2-248
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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