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2OHH
Asym. Unit
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
(3, 13)
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
8
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 not available)
All SNPs/Variants
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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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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.
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
(
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(
)
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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Homologous Superfamilies
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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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Organisms
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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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