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1FDI
Asym. Unit
Info
Asym.Unit (123 KB)
Biol.Unit 1 (117 KB)
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(1)
Title
:
OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE
Authors
:
P. D. Sun, J. C. Boyington
Date
:
28 Jan 97 (Deposition) - 20 Aug 97 (Release) - 06 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Selenium, Selenocysteine, Secys, Molybdenum, Molybdopterin, Mpt, Molybdopterin Guanine Dinucleotide, Mgd, Iron Sulfur Cluster, Fe4S4, Formate, Dehydrogenase, Anaerobic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. C. Boyington, V. N. Gladyshev, S. V. Khangulov, T. C. Stadtman, P. D. Sun
Crystal Structure Of Formate Dehydrogenase H: Catalysis Involving Mo, Molybdopterin, Selenocysteine, And An Fe4S4 Cluster.
Science V. 275 1305 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: MOLYBDENUM(VI) ION (6MOa)
2a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
2b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
3a: NITRITE ION (NO2a)
4a: (SECa)
5a: IRON/SULFUR CLUSTER (SF4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6MO
1
Ligand/Ion
MOLYBDENUM(VI) ION
2
MGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
3
NO2
1
Ligand/Ion
NITRITE ION
4
SEC
1
Mod. Amino Acid
5
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: FS4 (UNKNOWN)
7: MO4 (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SEC A:140 , HIS A:141 , ARG A:333 , GLY A:334 , GLN A:335 , VAL A:338 , 6MO A:803
BINDING SITE FOR RESIDUE NO2 A 804
2
AC2
SOFTWARE
CYS A:8 , TYR A:10 , CYS A:11 , SER A:13 , CYS A:15 , CYS A:42 , LYS A:44 , PRO A:182 , ILE A:183
BINDING SITE FOR RESIDUE SF4 A 800
3
AC3
SOFTWARE
ARG A:110 , GLY A:111 , THR A:112 , VAL A:139 , SEC A:140 , MET A:297 , GLN A:301 , GLN A:335 , GLY A:402 , GLU A:403 , ASP A:404 , THR A:408 , GLN A:428 , ASP A:429 , ILE A:430 , PHE A:431 , THR A:433 , SER A:445 , THR A:446 , HIS A:451 , ASP A:478 , THR A:579 , ARG A:581 , SER A:587 , CYS A:588 , TYR A:654 , CYS A:661 , ASN A:662 , TYR A:678 , MGD A:802 , 6MO A:803 , HOH A:829
BINDING SITE FOR RESIDUE MGD A 801
4
AC4
SOFTWARE
LYS A:44 , SEC A:140 , PHE A:173 , GLY A:174 , TYR A:175 , ASN A:176 , ASP A:179 , SER A:180 , CYS A:201 , ASP A:202 , PRO A:203 , ARG A:204 , LEU A:218 , GLY A:221 , ASN A:223 , GLY A:296 , MET A:297 , GLY A:298 , PHE A:302 , GLY A:334 , GLN A:335 , SER A:578 , VAL A:580 , ARG A:581 , GLU A:582 , VAL A:583 , HIS A:585 , TYR A:586 , SER A:587 , LYS A:679 , MGD A:801 , 6MO A:803 , HOH A:805 , HOH A:832
BINDING SITE FOR RESIDUE MGD A 802
5
AC5
SOFTWARE
SEC A:140 , MGD A:801 , MGD A:802 , NO2 A:804
BINDING SITE FOR RESIDUE 6MO A 803
6
FS4
UNKNOWN
SF4 A:800 , CYS A:8 , CYS A:11 , CYS A:15 , CYS A:42
THE IRON SULFUR CLUSTER IS COORDINATED TO THE SULFUR ATOMS OF CYS 8, CYS 11, CYS 15, AND CYS 42.
7
MO4
UNKNOWN
SEC A:140 , MGD A:801 , MGD A:802 , 6MO A:803 , NO2 A:804
THE MOLYBDENUM ATOM IS COORDINATED TO THE SELENIUM ATOM OF SEC 140, THE O1 OXYGEN ATOM OF NITRITE 804 AND THE FOUR SULFUR ATOMS OF MGD 801 AND MGD 802.
[
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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
(4, 4)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (A:1-56)
2: MOLYBDOPTERIN_PROK_1 (A:6-23)
3: MOLYBDOPTERIN_PROK_2 (A:433-450)
4: MOLYBDOPTERIN_PROK_3 (A:615-642)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
FDHF_ECOLI
1-56
1
A:1-56
2
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
FDHF_ECOLI
6-23
1
A:6-23
3
MOLYBDOPTERIN_PROK_2
PS00490
Prokaryotic molybdopterin oxidoreductases signature 2.
FDHF_ECOLI
433-450
1
A:433-450
4
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
FDHF_ECOLI
615-642
1
A:615-642
[
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1fdia1 (A:565-715)
2a: SCOP_d1fdia2 (A:1-564)
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Protein Domains
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Formate dehydrogenase H
(4)
Escherichia coli [TaxId: 562]
(4)
1a
d1fdia1
A:565-715
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Formate dehydrogenase H
(4)
Escherichia coli [TaxId: 562]
(4)
2a
d1fdia2
A:1-564
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CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1fdiA03 (A:141-333)
2a: CATH_1fdiA02 (A:59-139,A:334-529)
3a: CATH_1fdiA05 (A:689-715)
4a: CATH_1fdiA04 (A:568-688)
5a: CATH_1fdiA01 (A:1-58)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Escherichia coli. Organism_taxid: 562. Strain: fm911.
(3)
1a
1fdiA03
A:141-333
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Escherichia coli. Organism_taxid: 562. Strain: fm911.
(3)
2a
1fdiA02
A:59-139,A:334-529
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(7)
Escherichia coli. Organism_taxid: 562. Strain: fm911.
(2)
3a
1fdiA05
A:689-715
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Escherichia coli. Organism_taxid: 562. Strain: fm911.
(3)
4a
1fdiA04
A:568-688
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
ADC-like domains
(18)
Escherichia coli. Organism_taxid: 562. Strain: fm911.
(3)
5a
1fdiA01
A:1-58
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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