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2OHH
Biol. Unit 3
Info
Asym.Unit (291 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (144 KB)
Biol.Unit 3 (281 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF COENZYME F420H2 OXIDASE (FPRA), A DIIRON FLAVOPROTEIN, ACTIVE OXIDIZED STATE
Authors
:
H. Seedorf, E. Warkentin, U. Ermler
Date
:
10 Jan 07 (Deposition) - 22 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: A,B,D,E (1x)
Keywords
:
Beta-Lactamase Like Domain, Flavodoxine Like Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Seedorf, C. H. Hagemeier, S. Shima, R. K. Thauer, E. Warkentin, U. Ermler
Structure Of Coenzyme F420H2 Oxidase (Fpra), A Di-Iron Flavoprotein From Methanogenic Archaea Catalyzing The Reduction Of O2 To H2O.
Febs J. V. 274 1588 2007
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
2a: FLAVIN MONONUCLEOTIDE (FMNa)
2b: FLAVIN MONONUCLEOTIDE (FMNb)
2c: FLAVIN MONONUCLEOTIDE (FMNc)
2d: FLAVIN MONONUCLEOTIDE (FMNd)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
-1
Ligand/Ion
FE (III) ION
2
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
3
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:87 , HIS A:88 , ASP A:170 , HIS A:233 , FE A:502
BINDING SITE FOR RESIDUE FE A 501
02
AC2
SOFTWARE
HIS A:83 , GLU A:85 , HIS A:151 , ASP A:170 , FE A:501
BINDING SITE FOR RESIDUE FE A 502
03
AC3
SOFTWARE
ASP B:87 , HIS B:88 , ASP B:170 , HIS B:233 , FE B:1502
BINDING SITE FOR RESIDUE FE B 1501
04
AC4
SOFTWARE
HIS B:83 , GLU B:85 , HIS B:151 , ASP B:170 , FE B:1501
BINDING SITE FOR RESIDUE FE B 1502
05
AC5
SOFTWARE
ASP D:87 , HIS D:88 , ASP D:170 , HIS D:233 , SO4 D:2414 , FE D:2502
BINDING SITE FOR RESIDUE FE D 2501
06
AC6
SOFTWARE
HIS D:83 , GLU D:85 , HIS D:151 , ASP D:170 , SO4 D:2414 , FE D:2501
BINDING SITE FOR RESIDUE FE D 2502
07
AC7
SOFTWARE
ASP E:87 , HIS E:88 , ASP E:170 , HIS E:233 , FE E:3502 , HOH E:3971
BINDING SITE FOR RESIDUE FE E 3501
08
AC8
SOFTWARE
HIS E:83 , GLU E:85 , HIS E:151 , ASP E:170 , FE E:3501 , HOH E:3971
BINDING SITE FOR RESIDUE FE E 3502
09
AC9
SOFTWARE
TYR D:25 , HIS D:26 , GLU D:85 , ASP D:87 , HIS D:151 , ASP D:170 , HIS D:175 , LEU D:202 , HIS D:233 , FE D:2501 , FE D:2502
BINDING SITE FOR RESIDUE SO4 D 2414
10
BC1
SOFTWARE
THR A:265 , MET A:266 , HIS A:267 , GLY A:268 , SER A:269 , THR A:270 , PRO A:316 , THR A:317 , ILE A:318 , TYR A:319 , ASP A:320 , SER A:351 , MET A:352 , GLY A:353 , GLY A:354 , ASN A:355 , GLY A:356 , TYR A:381 , HOH A:736 , HOH A:887 , HIS B:26 , HIS B:151 , TRP B:152 , LEU B:202 , HOH B:1716
BINDING SITE FOR RESIDUE FMN A 701
11
BC2
SOFTWARE
GLU A:85 , HIS A:151 , TRP A:152 , LEU A:202 , THR B:265 , MET B:266 , HIS B:267 , GLY B:268 , SER B:269 , THR B:270 , PRO B:316 , THR B:317 , ILE B:318 , TYR B:319 , ASP B:320 , SER B:351 , MET B:352 , GLY B:353 , GLY B:354 , ASN B:355 , GLY B:356 , TYR B:381 , HOH B:1728 , HOH B:1731
BINDING SITE FOR RESIDUE FMN B 1701
12
BC3
SOFTWARE
THR D:265 , MET D:266 , HIS D:267 , GLY D:268 , SER D:269 , THR D:270 , PRO D:316 , THR D:317 , ILE D:318 , TYR D:319 , ASP D:320 , SER D:351 , MET D:352 , GLY D:353 , GLY D:354 , ASN D:355 , GLY D:356 , TYR D:381 , HOH D:2705 , HOH D:2793 , GLU E:85 , HIS E:151 , TRP E:152 , LEU E:202
BINDING SITE FOR RESIDUE FMN D 2701
13
BC4
SOFTWARE
GLU D:85 , HIS D:151 , TRP D:152 , LEU D:202 , HOH D:2886 , THR E:265 , MET E:266 , HIS E:267 , GLY E:268 , SER E:269 , THR E:270 , PRO E:316 , THR E:317 , ILE E:318 , TYR E:319 , ASP E:320 , SER E:351 , MET E:352 , GLY E:353 , GLY E:354 , ASN E:355 , GLY E:356 , TYR E:381 , HOH E:3730 , HOH E:3813
BINDING SITE FOR RESIDUE FMN E 3701
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: FLAVODOXIN_LIKE (A:259-399,B:259-399,D:259-399,E:25...)
2: FLAVODOXIN (A:261-277,B:261-277,D:261-277,E:26...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FLAVODOXIN_LIKE
PS50902
Flavodoxin-like domain profile.
FPRA_METTM
259-399
4
A:259-399
B:259-399
D:259-399
E:259-399
2
FLAVODOXIN
PS00201
Flavodoxin signature.
FPRA_METTM
261-277
4
A:261-277
B:261-277
D:261-277
E:261-277
[
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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
(2, 7)
Info
All SCOP Domains
1a: SCOP_d2ohha1 (A:1-254)
1b: SCOP_d2ohhb1 (B:1-254)
1c: SCOP_d2ohhd1 (D:1-254)
1d: SCOP_d2ohhe1 (E:1-254)
2a: SCOP_d2ohha2 (A:255-403)
2b: SCOP_d2ohhb2 (B:255-403)
2c: SCOP_d2ohhe2 (E:255-403)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-hydrolase/oxidoreductase
(184)
Superfamily
:
Metallo-hydrolase/oxidoreductase
(184)
Family
:
automated matches
(42)
Protein domain
:
automated matches
(42)
Methanothermobacter thermautotrophicus [TaxId: 145262]
(3)
1a
d2ohha1
A:1-254
1b
d2ohhb1
B:1-254
1c
d2ohhd1
D:1-254
1d
d2ohhe1
E:1-254
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Flavoproteins
(208)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Methanothermobacter thermautotrophicus [TaxId: 145262]
(3)
2a
d2ohha2
A:255-403
2b
d2ohhb2
B:255-403
2c
d2ohhe2
E:255-403
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2ohhA02 (A:258-401)
1b: CATH_2ohhB02 (B:258-401)
1c: CATH_2ohhD02 (D:258-401)
1d: CATH_2ohhE02 (E:258-401)
2a: CATH_2ohhA01 (A:1-252)
2b: CATH_2ohhB01 (B:1-252)
2c: CATH_2ohhD01 (D:1-252)
2d: CATH_2ohhE01 (E:1-252)
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)
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)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: dsmz2133.
(1)
1a
2ohhA02
A:258-401
1b
2ohhB02
B:258-401
1c
2ohhD02
D:258-401
1d
2ohhE02
E:258-401
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Metallo-beta-lactamase; Chain A
(92)
Homologous Superfamily
:
Metallo-beta-lactamase, chain A
(92)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: dsmz2133.
(1)
2a
2ohhA01
A:1-252
2b
2ohhB01
B:1-252
2c
2ohhD01
D:1-252
2d
2ohhE01
E:1-252
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Flavodoxin_1_2ohhE01 (E:261-395)
1b: PFAM_Flavodoxin_1_2ohhE02 (E:261-395)
1c: PFAM_Flavodoxin_1_2ohhE03 (E:261-395)
1d: PFAM_Flavodoxin_1_2ohhE04 (E:261-395)
2a: PFAM_Lactamase_B_2ohhE05 (E:30-275)
2b: PFAM_Lactamase_B_2ohhE06 (E:30-275)
2c: PFAM_Lactamase_B_2ohhE07 (E:30-275)
2d: PFAM_Lactamase_B_2ohhE08 (E:30-275)
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)
Clan
:
Flavoprotein
(71)
Family
:
Flavodoxin_1
(23)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(2)
1a
Flavodoxin_1-2ohhE01
E:261-395
1b
Flavodoxin_1-2ohhE02
E:261-395
1c
Flavodoxin_1-2ohhE03
E:261-395
1d
Flavodoxin_1-2ohhE04
E:261-395
Clan
:
Metallo-HOrase
(67)
Family
:
Lactamase_B
(53)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(2)
2a
Lactamase_B-2ohhE05
E:30-275
2b
Lactamase_B-2ohhE06
E:30-275
2c
Lactamase_B-2ohhE07
E:30-275
2d
Lactamase_B-2ohhE08
E:30-275
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Asym.Unit (291 KB)
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