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1UBT
Asym. Unit
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Asym.Unit (280 KB)
Biol.Unit 1 (276 KB)
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(1)
Title
:
THREE-DIMENSIONAL STRUCTURE OF THE CARBON MONOXIDE COMPLEX OF [NIFE]HYDROGENASE FROM DESULUFOVIBRIO VULGARIS MIYAZAKI F
Authors
:
H. Ogata, Y. Mizoguchi, N. Mizuno, K. Miki, S. Adachi, N. Yasuoka, T. Yagi, O. Yamauchi, S. Hirota, Y. Higuchi
Date
:
04 Apr 03 (Deposition) - 29 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.34
Chains
:
Asym. Unit : L,S
Biol. Unit 1: L,S (1x)
Keywords
:
High Resolution Crystal Structure, [Nife]Hydrogenase, Oxidoreductase, Carbon Monoxide Complex
(Keyword Search:
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]
)
Reference
:
H. Ogata, Y. Mizoguchi, N. Mizuno, K. Miki, S. Adachi, N. Yasuoka, T. Yagi, O. Yamauchi, S. Hirota, Y. Higuchi
Structural Studies Of The Carbon Monoxide Complex Of [Nife]Hydrogenase From Desulfovibrio Vulgaris Miyazaki F: Suggestion For The Initial Activation Site For Dihydrogen
J. Am. Chem. Soc. V. 124 11628 2002
(for further references see the
PDB file header
)
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Hetero Components
(4, 5)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
2a: (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICA... (FNEa)
3a: MAGNESIUM ION (MGa)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
FNE
1
Ligand/Ion
(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU L:62 , LEU L:498 , HIS L:552 , HOH L:3001 , HOH L:3002 , HOH L:3003
BINDING SITE FOR RESIDUE MG L 1005
2
AC2
SOFTWARE
ARG L:79 , HIS L:235 , GLU S:16 , CYS S:17 , CYS S:20 , THR S:113 , CYS S:114 , GLY S:149 , CYS S:150 , PRO S:151
BINDING SITE FOR RESIDUE SF4 S 1001
3
AC3
SOFTWARE
HIS S:188 , CYS S:191 , ARG S:193 , LEU S:194 , CYS S:216 , LEU S:217 , CYS S:222
BINDING SITE FOR RESIDUE SF4 S 1002
4
AC4
SOFTWARE
LYS L:232 , GLN L:237 , THR S:227 , ASN S:229 , CYS S:231 , PHE S:236 , TRP S:241 , CYS S:249 , ILE S:250 , CYS S:252
BINDING SITE FOR RESIDUE F3S S 1003
5
AC5
SOFTWARE
CYS L:81 , CYS L:84 , HIS L:88 , ALA L:477 , PRO L:478 , ARG L:479 , LEU L:482 , VAL L:500 , PRO L:501 , SER L:502 , CYS L:546 , CYS L:549
BINDING SITE FOR RESIDUE FNE L 1004
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (L:59-84)
2: NI_HGENASE_L_2 (L:543-552)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NI_HGENASE_L_1
PS00507
Nickel-dependent hydrogenases large subunit signature 1.
PHNL_DESVM
59-84
1
L:59-84
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESVM
543-552
1
L:543-552
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Exons
(0, 0)
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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_d1ubts_ (S:)
2a: SCOP_d1ubtl_ (L:)
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Folds
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Superfamilies
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)
(
)
Families
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
Nickel-iron hydrogenase, small subunit
(16)
Desulfovibrio vulgaris [TaxId: 881]
(11)
1a
d1ubts_
S:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
Nickel-iron hydrogenase, large subunit
(17)
Desulfovibrio vulgaris [TaxId: 881]
(11)
2a
d1ubtl_
L:
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1ubtS01 (S:3-182)
2a: CATH_1ubtS02 (S:183-267)
3a: CATH_1ubtL00 (L:19-552)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.700, no name defined]
(28)
'miyazaki f' (Desulfovibrio vulgaris str)
(16)
1a
1ubtS01
S:3-182
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome-c3 Hydrogenase; Chain A, domain 2
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain A, domain 2
(28)
'miyazaki f' (Desulfovibrio vulgaris str)
(16)
2a
1ubtS02
S:183-267
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
'miyazaki f' (Desulfovibrio vulgaris str)
(16)
3a
1ubtL00
L:19-552
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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