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1YQ9
Biol. Unit 2
Info
Asym.Unit (271 KB)
Biol.Unit 1 (135 KB)
Biol.Unit 2 (132 KB)
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(1)
Title
:
STRUCTURE OF THE UNREADY OXIDIZED FORM OF [NIFE] HYDROGENASE
Authors
:
A. Volbeda, L. Martin, C. Cavazza, M. Matho, B. W. Faber, W. Roseboom, S. P. Albracht, E. Garcin, M. Rousset, J. C. Fontecilla-Camps
Date
:
01 Feb 05 (Deposition) - 19 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,H,I
Biol. Unit 1: A,H (1x)
Biol. Unit 2: B,I (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, L. Martin, C. Cavazza, M. Matho, B. W. Faber, W. Roseboom, S. P. Albracht, E. Garcin, M. Rousset, J. C. Fontecilla-Camps
Structural Differences Between The Ready And Unready Oxidized States Of [Nife] Hydrogenases.
J. Biol. Inorg. Chem. V. 10 239 2005
(for further references see the
PDB file header
)
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Hetero Components
(6, 8)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
2b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: HYDROSULFURIC ACID (H2Sa)
4b: HYDROSULFURIC ACID (H2Sb)
4c: HYDROSULFURIC ACID (H2Sc)
4d: HYDROSULFURIC ACID (H2Sd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
7a: PEROXIDE ION (PERa)
7b: PEROXIDE ION (PERb)
8a: IRON/SULFUR CLUSTER (SF4a)
8b: IRON/SULFUR CLUSTER (SF4b)
8c: IRON/SULFUR CLUSTER (SF4c)
8d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
3
GOL
1
Ligand/Ion
GLYCEROL
4
H2S
2
Ligand/Ion
HYDROSULFURIC ACID
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NI
-1
Ligand/Ion
NICKEL (II) ION
7
PER
1
Ligand/Ion
PEROXIDE ION
8
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC3 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
CYS I:65 , CYS I:68 , CYS I:530 , CYS I:533 , FCO I:537 , PER I:539
BINDING SITE FOR RESIDUE NI I 538
02
AC4
SOFTWARE
GLU I:46 , LEU I:482 , HIS I:536 , HOH I:5024 , HOH I:5025 , HOH I:5026
BINDING SITE FOR RESIDUE MG I 540
03
BC3
SOFTWARE
HIS B:185 , CYS B:188 , ARG B:190 , LEU B:191 , CYS B:213 , LEU B:214 , CYS B:219
BINDING SITE FOR RESIDUE SF4 B 265
04
BC4
SOFTWARE
ASN B:226 , CYS B:228 , PHE B:233 , TRP B:238 , CYS B:246 , ILE B:247 , CYS B:249 , LYS I:216 , GLN I:221
BINDING SITE FOR RESIDUE F3S B 266
05
BC5
SOFTWARE
CYS B:17 , CYS B:20 , GLY B:110 , THR B:111 , CYS B:112 , GLY B:147 , CYS B:148 , PRO B:149 , ARG I:63
BINDING SITE FOR RESIDUE SF4 B 267
06
BC6
SOFTWARE
TYR B:115 , GLY B:117 , ASN B:253 , HOH B:291
BINDING SITE FOR RESIDUE H2S B 2268
07
BC7
SOFTWARE
CYS I:68 , HIS I:72 , ALA I:461 , PRO I:462 , ARG I:463 , VAL I:484 , PRO I:485 , SER I:486 , CYS I:533 , NI I:538 , PER I:539
BINDING SITE FOR RESIDUE FCO I 537
08
BC8
SOFTWARE
CYS I:68 , ARG I:463 , CYS I:530 , CYS I:533 , FCO I:537 , NI I:538
BINDING SITE FOR RESIDUE PER I 539
09
BC9
SOFTWARE
ARG I:55 , VAL I:224 , VAL I:225 , HOH I:5061 , HOH I:5071
BINDING SITE FOR RESIDUE H2S I 2541
10
CC1
SOFTWARE
HIS A:54 , GLY A:88 , ARG A:90 , GOL A:1272 , HOH A:1562 , PHE B:194
BINDING SITE FOR RESIDUE GOL A 1271
11
CC2
SOFTWARE
GLU A:57 , LEU A:60 , HIS A:61 , ILE A:64 , ARG A:90 , GLU A:98 , GOL A:1271 , PHE B:194 , TYR B:215
BINDING SITE FOR RESIDUE GOL A 1272
12
CC3
SOFTWARE
LYS A:102 , HOH A:1639 , HOH A:1642 , LEU B:257 , ALA B:264 , HOH B:313 , HOH B:328
BINDING SITE FOR RESIDUE GOL A 1273
13
CC5
SOFTWARE
GLY A:89 , GLY B:197 , HOH B:326 , HOH B:355 , GLU H:347 , PHE H:348 , HOH H:5136
BINDING SITE FOR RESIDUE GOL H 1543
14
CC7
SOFTWARE
ALA B:208 , LYS B:209 , GLY B:211 , HOH B:375 , ASP I:232
BINDING SITE FOR RESIDUE GOL B 2542
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (I:43-68)
2: NI_HGENASE_L_2 (I:527-536)
;
View:
Select:
Label:
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_DESGI
43-68
1
-
I:43-68
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESGI
527-536
1
-
I:527-536
[
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 4)
Info
All SCOP Domains
1a: SCOP_d1yq9a_ (A:)
1b: SCOP_d1yq9b_ (B:)
2a: SCOP_d1yq9i_ (I:)
3a: SCOP_d1yq9h1 (H:7-536)
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(
)
(
)
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(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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 gigas [TaxId: 879]
(1)
1a
d1yq9a_
A:
1b
d1yq9b_
B:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfovibrio gigas [TaxId: 879]
(1)
2a
d1yq9i_
I:
Protein domain
:
Nickel-iron hydrogenase, large subunit
(17)
Desulfovibrio gigas [TaxId: 879]
(3)
3a
d1yq9h1
H:7-536
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1yq9A01 (A:4-179)
1b: CATH_1yq9B01 (B:5-179)
2a: CATH_1yq9A02 (A:180-264)
2b: CATH_1yq9B02 (B:180-264)
3a: CATH_1yq9H00 (H:7-536)
3b: CATH_1yq9I00 (I:7-536)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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 gigas. Organism_taxid: 879. Strain: wild type.
(1)
1a
1yq9A01
A:4-179
1b
1yq9B01
B:5-179
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 gigas. Organism_taxid: 879. Strain: wild type.
(1)
2a
1yq9A02
A:180-264
2b
1yq9B02
B:180-264
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio gigas. Organism_taxid: 879. Strain: wild type.
(1)
3a
1yq9H00
H:7-536
3b
1yq9I00
I:7-536
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_1yq9I01 (I:43-535)
1b: PFAM_NiFeSe_Hases_1yq9I02 (I:43-535)
2a: PFAM_Oxidored_q6_1yq9B01 (B:17-162)
2b: PFAM_Oxidored_q6_1yq9B02 (B:17-162)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Desulfovibrio gigas
(1)
1a
NiFeSe_Hases-1yq9I01
I:43-535
1b
NiFeSe_Hases-1yq9I02
I:43-535
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Desulfovibrio gigas
(1)
2a
Oxidored_q6-1yq9B01
B:17-162
2b
Oxidored_q6-1yq9B02
B:17-162
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Asymmetric Unit 1
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Asym.Unit (271 KB)
Header - Asym.Unit
Biol.Unit 1 (135 KB)
Header - Biol.Unit 1
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