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1FFV
Asym. Unit
Info
Asym.Unit (419 KB)
Biol.Unit 1 (411 KB)
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(1)
Title
:
CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA
Authors
:
P. Haenzelmann, H. Dobbek, L. Gremer, R. Huber, O. Meyer
Date
:
26 Jul 00 (Deposition) - 15 Sep 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Hydrolase, Dehydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Hanzelmann, H. Dobbek, L. Gremer, R. Huber, O. Meyer
The Effect Of Intracellular Molybdenum In Hydrogenophaga Pseudoflava On The Crystallographic Structure Of The Seleno-Molybdo-Iron-Sulfur Flavoenzyme Carbon Monoxide Dehydrogenase.
J. Mol. Biol. V. 301 1221 2000
(for further references see the
PDB file header
)
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: C-GAMMA-HYDROXY ARGININE (AROa)
1b: C-GAMMA-HYDROXY ARGININE (AROb)
2a: S-SELANYL CYSTEINE (CSZa)
2b: S-SELANYL CYSTEINE (CSZb)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4c: FE2/S2 (INORGANIC) CLUSTER (FESc)
4d: FE2/S2 (INORGANIC) CLUSTER (FESd)
5a: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTI... (PCDa)
5b: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTI... (PCDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ARO
2
Mod. Amino Acid
C-GAMMA-HYDROXY ARGININE
2
CSZ
2
Mod. Amino Acid
S-SELANYL CYSTEINE
3
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
PCD
2
Ligand/Ion
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:100 , CYS A:101 , GLY A:102 , CYS A:104 , CYS A:136 , ARG A:137 , CYS A:138
BINDING SITE FOR RESIDUE FES A 1907
2
AC2
SOFTWARE
GLY A:41 , CYS A:42 , SER A:45 , HIS A:46 , CYS A:47 , GLY A:48 , CYS A:50 , LYS A:60 , CYS A:62
BINDING SITE FOR RESIDUE FES A 1908
3
AC3
SOFTWARE
GLN D:100 , CYS D:101 , GLY D:102 , CYS D:104 , CYS D:136 , ARG D:137 , CYS D:138
BINDING SITE FOR RESIDUE FES D 1909
4
AC4
SOFTWARE
GLY D:41 , CYS D:42 , SER D:45 , HIS D:46 , CYS D:47 , GLY D:48 , CYS D:50 , LYS D:60 , CYS D:62
BINDING SITE FOR RESIDUE FES D 1910
5
AC5
SOFTWARE
GLN A:100 , CYS A:138 , GLN B:237 , GLY B:266 , GLY B:267 , PHE B:268 , GLY B:269 , ALA B:382 , TYR B:383 , ARO B:384 , CSZ B:385 , GLN B:522 , GLY B:523 , GLN B:524 , HIS B:526 , THR B:529 , TYR B:562 , GLY B:563 , SER B:564 , ARG B:565 , SER B:566 , THR B:567 , CYS B:680 , THR B:682 , ILE B:684 , ASN B:685 , ILE B:688 , ILE B:689 , GLN B:692 , LYS B:753 , GLY B:754 , VAL B:755 , ALA B:756 , GLU B:757 , HOH B:2240 , HOH B:2389 , HOH B:2390 , HOH B:2391
BINDING SITE FOR RESIDUE PCD B 1920
6
AC6
SOFTWARE
GLN D:100 , CYS D:138 , GLN E:237 , GLY E:266 , GLY E:267 , PHE E:268 , GLY E:269 , ALA E:382 , TYR E:383 , ARO E:384 , CSZ E:385 , GLN E:522 , GLY E:523 , GLN E:524 , HIS E:526 , THR E:529 , THR E:561 , TYR E:562 , GLY E:563 , SER E:564 , ARG E:565 , SER E:566 , THR E:567 , CYS E:680 , THR E:682 , ILE E:684 , ASN E:685 , ILE E:689 , GLN E:692 , LYS E:753 , GLY E:754 , VAL E:755 , ALA E:756 , GLU E:757 , HOH E:2087 , HOH E:2188 , HOH E:2355 , HOH E:2367 , HOH E:2414
BINDING SITE FOR RESIDUE PCD E 1921
7
AC7
SOFTWARE
SER A:45 , HIS A:46 , LYS C:29 , LEU C:30 , ALA C:32 , GLY C:33 , GLY C:34 , HIS C:35 , SER C:36 , LEU C:37 , ILE C:101 , ALA C:102 , GLY C:110 , THR C:111 , GLY C:114 , ASP C:115 , ALA C:117 , HIS C:118 , ASN C:123 , ASP C:124 , LEU C:161 , VAL C:166 , MET C:167 , LYS C:185 , GLY C:191 , ASP C:192 , TRP C:193 , HOH C:1981 , HOH C:2007 , HOH C:2024 , HOH C:2046
BINDING SITE FOR RESIDUE FAD C 1922
8
AC8
SOFTWARE
SER D:45 , LYS F:29 , LEU F:30 , ALA F:32 , GLY F:33 , GLY F:34 , HIS F:35 , SER F:36 , LEU F:37 , ILE F:54 , ILE F:101 , ALA F:102 , GLY F:110 , THR F:111 , GLY F:114 , ASP F:115 , ALA F:117 , ASN F:123 , ASP F:124 , LEU F:161 , VAL F:166 , MET F:167 , LYS F:185 , GLY F:191 , ASP F:192 , TRP F:193 , HOH F:1961 , HOH F:1967 , HOH F:2013 , HOH F:2017
BINDING SITE FOR RESIDUE FAD F 1923
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: FAD_PCMH (C:1-177,F:1-177)
2: 2FE2S_FER_2 (A:4-80,D:4-80)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
DCMM_HYDPS
1-177
2
C:1-177
F:1-177
2
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
DCMS_HYDPS
4-80
2
A:4-80
D:4-80
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1ffva1 (A:82-157)
1b: SCOP_d1ffvd1 (D:82-157)
2a: SCOP_d1ffvb1 (B:7-146)
2b: SCOP_d1ffve1 (E:7-146)
3a: SCOP_d1ffva2 (A:3-81)
3b: SCOP_d1ffvd2 (D:2-81)
4a: SCOP_d1ffvc1 (C:178-287)
4b: SCOP_d1ffvf1 (F:178-287)
5a: SCOP_d1ffvc2 (C:1-177)
5b: SCOP_d1ffvf2 (F:1-177)
6a: SCOP_d1ffvb2 (B:147-803)
6b: SCOP_d1ffve2 (E:147-803)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Carbon monoxide (CO) dehydrogenase iron-sulfur protein, C-domain
(8)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
1a
d1ffva1
A:82-157
1b
d1ffvd1
D:82-157
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain
(7)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
2a
d1ffvb1
B:7-146
2b
d1ffve1
E:7-146
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain
(8)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
3a
d1ffva2
A:3-81
3b
d1ffvd2
D:2-81
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
CO dehydrogenase flavoprotein C-terminal domain-like
(23)
Protein domain
:
Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain
(8)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
4a
d1ffvc1
C:178-287
4b
d1ffvf1
F:178-287
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
CO dehydrogenase flavoprotein N-terminal domain-like
(33)
Protein domain
:
Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain
(8)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
5a
d1ffvc2
C:1-177
5b
d1ffvf2
F:1-177
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Carbon monoxide (CO) dehydrogenase molybdoprotein
(7)
Hydrogenophaga pseudoflava [TaxId: 47421]
(2)
6a
d1ffvb2
B:147-803
6b
d1ffve2
E:147-803
[
close SCOP info
]
CATH Domains
(7, 20)
Info
all CATH domains
1a: CATH_1ffvB03 (B:484-649)
1b: CATH_1ffvE03 (E:484-649)
1c: CATH_1ffvB04 (B:440-483,B:650-803)
1d: CATH_1ffvE04 (E:440-483,E:650-803)
1e: CATH_1ffvB02 (B:142-209,B:307-383)
1f: CATH_1ffvE02 (E:142-209,E:307-383)
1g: CATH_1ffvB05 (B:210-306)
1h: CATH_1ffvE05 (E:210-306)
2a: CATH_1ffvC02 (C:180-284)
2b: CATH_1ffvF02 (F:180-284)
3a: CATH_1ffvC01 (C:1-54)
3b: CATH_1ffvF01 (F:1-54)
4a: CATH_1ffvC03 (C:60-173)
4b: CATH_1ffvF03 (F:60-173)
5a: CATH_1ffvB01 (B:7-141)
5b: CATH_1ffvE01 (E:7-141)
6a: CATH_1ffvA01 (A:3-76)
6b: CATH_1ffvD01 (D:3-76)
7a: CATH_1ffvA02 (A:81-156)
7b: CATH_1ffvD02 (D:81-156)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Aldehyde Oxidoreductase; domain 4
(20)
Homologous Superfamily
:
Aldehyde Oxidoreductase; domain 4
(20)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
1a
1ffvB03
B:484-649
1b
1ffvE03
E:484-649
1c
1ffvB04
B:440-483,B:650-803
1d
1ffvE04
E:440-483,E:650-803
1e
1ffvB02
B:142-209,B:307-383
1f
1ffvE02
E:142-209,E:307-383
1g
1ffvB05
B:210-306
1h
1ffvE05
E:210-306
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.50, no name defined]
(22)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
2a
1ffvC02
C:180-284
2b
1ffvF02
F:180-284
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
3a
1ffvC01
C:1-54
3b
1ffvF01
F:1-54
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
4a
1ffvC03
C:60-173
4b
1ffvF03
F:60-173
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.50, no name defined]
(20)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
5a
1ffvB01
B:7-141
5b
1ffvE01
E:7-141
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
6a
1ffvA01
A:3-76
6b
1ffvD01
D:3-76
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Hydrogenophaga pseudoflava. Organism_taxid: 47421. Hydrogenophaga pseudoflava. Organism_taxid: 47421.
(2)
7a
1ffvA02
A:81-156
7b
1ffvD02
D:81-156
[
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Pfam Domains
(0, 0)
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all PFAM domains
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