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2OHI
Biol. Unit 6
Info
Asym.Unit (527 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (137 KB)
Biol.Unit 3 (136 KB)
Biol.Unit 4 (135 KB)
Biol.Unit 5 (261 KB)
Biol.Unit 6 (263 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF COENZYME F420H2 OXIDASE (FPRA), A DIIRON FLAVOPROTEIN, REDUCED 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
:
2.30
Chains
:
Asym. Unit : A,B,D,E,G,H,I,J
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: G,H (1x)
Biol. Unit 4: I,J (1x)
Biol. Unit 5: G,H,I,J (1x)
Biol. Unit 6: 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
(1, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
2g: FE (III) ION (FEg)
2h: FE (III) ION (FEh)
2i: FE (III) ION (FEi)
2j: FE (III) ION (FEj)
2k: FE (III) ION (FEk)
2l: FE (III) ION (FEl)
2m: FE (III) ION (FEm)
2n: FE (III) ION (FEn)
2o: FE (III) ION (FEo)
2p: FE (III) ION (FEp)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
3b: FLAVIN MONONUCLEOTIDE (FMNb)
3c: FLAVIN MONONUCLEOTIDE (FMNc)
3d: FLAVIN MONONUCLEOTIDE (FMNd)
3e: FLAVIN MONONUCLEOTIDE (FMNe)
3f: FLAVIN MONONUCLEOTIDE (FMNf)
3g: FLAVIN MONONUCLEOTIDE (FMNg)
3h: FLAVIN MONONUCLEOTIDE (FMNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
FE
-1
Ligand/Ion
FE (III) ION
3
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
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Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC6 (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:503
BINDING SITE FOR RESIDUE FE A 501
02
AC2
SOFTWARE
ASP B:87 , HIS B:88 , ASP B:170 , HIS B:233 , HOH B:1739
BINDING SITE FOR RESIDUE FE B 1501
03
AC3
SOFTWARE
ASP D:87 , HIS D:88 , ASP D:170 , HIS D:233 , HOH D:2743
BINDING SITE FOR RESIDUE FE D 2501
04
AC4
SOFTWARE
ASP E:87 , HIS E:88 , ASP E:170 , HIS E:233
BINDING SITE FOR RESIDUE FE E 3501
05
AC9
SOFTWARE
HIS A:83 , GLU A:85 , HIS A:151 , ASP A:170 , FE A:501
BINDING SITE FOR RESIDUE FE A 503
06
BC1
SOFTWARE
HIS B:83 , GLU B:85 , HIS B:151 , ASP B:170
BINDING SITE FOR RESIDUE FE B 1503
07
BC2
SOFTWARE
HIS D:83 , GLU D:85 , HIS D:151 , ASP D:170
BINDING SITE FOR RESIDUE FE D 2503
08
BC3
SOFTWARE
HIS E:83 , GLU E:85 , HIS E:151 , ASP E:170
BINDING SITE FOR RESIDUE FE E 3503
09
CC1
SOFTWARE
ARG D:340
BINDING SITE FOR RESIDUE CL D 2504
10
CC3
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:709 , HOH A:732 , GLU B:85 , TRP B:152
BINDING SITE FOR RESIDUE FMN A 701
11
CC4
SOFTWARE
HIS A:151 , TRP A:152 , 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:1717 , HOH B:1723
BINDING SITE FOR RESIDUE FMN B 1701
12
CC5
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:2735 , GLU E:85 , TRP E:152
BINDING SITE FOR RESIDUE FMN D 2701
13
CC6
SOFTWARE
TRP D:152 , 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
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:
Select:
Label:
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:
Select:
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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All Exon Boundaries
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Label:
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, 16)
Info
All SCOP Domains
1a: SCOP_d2ohia1 (A:1-254)
1b: SCOP_d2ohid1 (D:1-254)
1c: SCOP_d2ohie1 (E:1-254)
1d: SCOP_d2ohig1 (G:1-254)
1e: SCOP_d2ohih1 (H:1-254)
1f: SCOP_d2ohii1 (I:1-254)
1g: SCOP_d2ohij1 (J:1-254)
1h: SCOP_d2ohib1 (B:1-254)
2a: SCOP_d2ohia2 (A:255-403)
2b: SCOP_d2ohie2 (E:255-403)
2c: SCOP_d2ohig2 (G:255-403)
2d: SCOP_d2ohih2 (H:255-403)
2e: SCOP_d2ohii2 (I:255-403)
2f: SCOP_d2ohij2 (J:255-403)
2g: SCOP_d2ohib2 (B:255-403)
2h: SCOP_d2ohid2 (D:255-403)
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Classes
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)
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)
Folds
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(
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Superfamilies
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)
(
)
Families
(
)
(
)
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
d2ohia1
A:1-254
1b
d2ohid1
D:1-254
1c
d2ohie1
E:1-254
1d
d2ohig1
G:1-254
1e
d2ohih1
H:1-254
1f
d2ohii1
I:1-254
1g
d2ohij1
J:1-254
1h
d2ohib1
B: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
d2ohia2
A:255-403
2b
d2ohie2
E:255-403
2c
d2ohig2
G:255-403
2d
d2ohih2
H:255-403
2e
d2ohii2
I:255-403
2f
d2ohij2
J:255-403
2g
d2ohib2
B:255-403
2h
d2ohid2
D:255-403
[
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]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_2ohiA02 (A:258-401)
1b: CATH_2ohiI02 (I:258-401)
1c: CATH_2ohiJ02 (J:258-401)
1d: CATH_2ohiB02 (B:258-401)
1e: CATH_2ohiD02 (D:258-401)
1f: CATH_2ohiE02 (E:258-401)
1g: CATH_2ohiG02 (G:258-401)
1h: CATH_2ohiH02 (H:258-401)
2a: CATH_2ohiA01 (A:1-252)
2b: CATH_2ohiI01 (I:1-252)
2c: CATH_2ohiJ01 (J:1-252)
2d: CATH_2ohiB01 (B:1-252)
2e: CATH_2ohiD01 (D:1-252)
2f: CATH_2ohiE01 (E:1-252)
2g: CATH_2ohiG01 (G:1-252)
2h: CATH_2ohiH01 (H:1-252)
View:
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)
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)
(
)
Topologies
(
)
(
)
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)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: dszm2133.
(2)
1a
2ohiA02
A:258-401
1b
2ohiI02
I:258-401
1c
2ohiJ02
J:258-401
1d
2ohiB02
B:258-401
1e
2ohiD02
D:258-401
1f
2ohiE02
E:258-401
1g
2ohiG02
G:258-401
1h
2ohiH02
H: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: dszm2133.
(2)
2a
2ohiA01
A:1-252
2b
2ohiI01
I:1-252
2c
2ohiJ01
J:1-252
2d
2ohiB01
B:1-252
2e
2ohiD01
D:1-252
2f
2ohiE01
E:1-252
2g
2ohiG01
G:1-252
2h
2ohiH01
H:1-252
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Flavodoxin_1_2ohiJ01 (J:261-395)
1b: PFAM_Flavodoxin_1_2ohiJ02 (J:261-395)
1c: PFAM_Flavodoxin_1_2ohiJ03 (J:261-395)
1d: PFAM_Flavodoxin_1_2ohiJ04 (J:261-395)
1e: PFAM_Flavodoxin_1_2ohiJ05 (J:261-395)
1f: PFAM_Flavodoxin_1_2ohiJ06 (J:261-395)
1g: PFAM_Flavodoxin_1_2ohiJ07 (J:261-395)
1h: PFAM_Flavodoxin_1_2ohiJ08 (J:261-395)
2a: PFAM_Lactamase_B_2ohiJ09 (J:30-275)
2b: PFAM_Lactamase_B_2ohiJ10 (J:30-275)
2c: PFAM_Lactamase_B_2ohiJ11 (J:30-275)
2d: PFAM_Lactamase_B_2ohiJ12 (J:30-275)
2e: PFAM_Lactamase_B_2ohiJ13 (J:30-275)
2f: PFAM_Lactamase_B_2ohiJ14 (J:30-275)
2g: PFAM_Lactamase_B_2ohiJ15 (J:30-275)
2h: PFAM_Lactamase_B_2ohiJ16 (J:30-275)
View:
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Clans
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Flavoprotein
(71)
Family
:
Flavodoxin_1
(23)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(2)
1a
Flavodoxin_1-2ohiJ01
J:261-395
1b
Flavodoxin_1-2ohiJ02
J:261-395
1c
Flavodoxin_1-2ohiJ03
J:261-395
1d
Flavodoxin_1-2ohiJ04
J:261-395
1e
Flavodoxin_1-2ohiJ05
J:261-395
1f
Flavodoxin_1-2ohiJ06
J:261-395
1g
Flavodoxin_1-2ohiJ07
J:261-395
1h
Flavodoxin_1-2ohiJ08
J: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-2ohiJ09
J:30-275
2b
Lactamase_B-2ohiJ10
J:30-275
2c
Lactamase_B-2ohiJ11
J:30-275
2d
Lactamase_B-2ohiJ12
J:30-275
2e
Lactamase_B-2ohiJ13
J:30-275
2f
Lactamase_B-2ohiJ14
J:30-275
2g
Lactamase_B-2ohiJ15
J:30-275
2h
Lactamase_B-2ohiJ16
J:30-275
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