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3CUS
Biol. Unit 3
Info
Asym.Unit (399 KB)
Biol.Unit 1 (135 KB)
Biol.Unit 2 (134 KB)
Biol.Unit 3 (134 KB)
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(1)
Title
:
STRUCTURE OF A DOUBLE ILE/PHE MUTANT OF NI-FE HYDROGENASE REFINED AT 2.2 ANGSTROM RESOLUTION
Authors
:
A. Volbeda
Date
:
17 Apr 08 (Deposition) - 05 Aug 08 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: B,R (1x)
Biol. Unit 3: C,S (1x)
Keywords
:
Ni-Fe Hydrogenase Tunnel Mutant, Iron, Iron-Sulfur, Metal-Binding, Oxidoreductase, Nickel
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Leroux, S. Dementin, B. Burlat, L. Cournac, A. Volbeda, S. Champ, L. Martin, B. Guigliarelli, P. Bertrand, J. Fontecilla-Camps, M. Rousset
Experimental Approaches To Kinetics Of Gas Diffusion In Hydrogenase
Proc. Natl. Acad. Sci. Usa V. 105 11188 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
1c: S-HYDROXYCYSTEINE (CSOc)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
3a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
6c: NICKEL (II) ION (NIc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
7e: IRON/SULFUR CLUSTER (SF4e)
7f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
GOL
1
Ligand/Ion
GLYCEROL
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NI
-1
Ligand/Ion
NICKEL (II) ION
7
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(8, 8)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: BC6 (SOFTWARE)
4: BC7 (SOFTWARE)
5: BC8 (SOFTWARE)
6: BC9 (SOFTWARE)
7: CC3 (SOFTWARE)
8: CC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
CYS S:72 , CYS S:75 , CYS S:546
BINDING SITE FOR RESIDUE NI S 551
2
AC6
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:562 , HOH S:563 , HOH S:564
BINDING SITE FOR RESIDUE MG S 553
3
BC6
SOFTWARE
HIS C:184 , CYS C:187 , ARG C:189 , LEU C:190 , CYS C:212 , LEU C:213 , CYS C:218
BINDING SITE FOR RESIDUE SF4 C 265
4
BC7
SOFTWARE
ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , GLN S:230
BINDING SITE FOR RESIDUE F3S C 266
5
BC8
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , PRO C:148 , ARG S:70 , HIS S:228
BINDING SITE FOR RESIDUE SF4 C 267
6
BC9
SOFTWARE
CYS S:75 , HIS S:79 , ALA S:474 , PRO S:475 , ARG S:476 , LEU S:479 , PRO S:498 , SER S:499 , CYS S:546
BINDING SITE FOR RESIDUE FCO S 550
7
CC3
SOFTWARE
ALA A:55 , PHE C:198 , ASN Q:181 , ALA Q:182 , LEU Q:185 , ARG Q:529 , HOH Q:567
BINDING SITE FOR RESIDUE GOL Q 562
8
CC5
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , THR S:297 , GLU S:445 , HOH S:583 , HOH S:724
BINDING SITE FOR RESIDUE GOL S 561
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (S:50-75)
2: NI_HGENASE_L_2 (S:540-549)
;
View:
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End label:
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_DESFR
50-75
1
-
-
S:50-75
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
1
-
-
S:540-549
[
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]
Exons
(0, 0)
Info
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3cusa_ (A:)
1b: SCOP_d3cusb_ (B:)
1c: SCOP_d3cusc_ (C:)
2a: SCOP_d3cusq_ (Q:)
2b: SCOP_d3cusr_ (R:)
2c: SCOP_d3cuss_ (S:)
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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
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
1a
d3cusa_
A:
1b
d3cusb_
B:
1c
d3cusc_
C:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
2a
d3cusq_
Q:
2b
d3cusr_
R:
2c
d3cuss_
S:
[
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]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_3cusA01 (A:3-178)
1b: CATH_3cusB01 (B:3-178)
1c: CATH_3cusC01 (C:5-178)
2a: CATH_3cusA02 (A:179-263)
2b: CATH_3cusB02 (B:179-263)
2c: CATH_3cusC02 (C:179-263)
3a: CATH_3cusQ00 (Q:6-549)
3b: CATH_3cusS00 (S:6-549)
3c: CATH_3cusR00 (R:5-549)
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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)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
1a
3cusA01
A:3-178
1b
3cusB01
B:3-178
1c
3cusC01
C:5-178
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)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
2a
3cusA02
A:179-263
2b
3cusB02
B:179-263
2c
3cusC02
C:179-263
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
3a
3cusQ00
Q:6-549
3b
3cusS00
S:6-549
3c
3cusR00
R:5-549
[
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Pfam Domains
(0, 0)
Info
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Asymmetric Unit 1
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Asym.Unit (399 KB)
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