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1YRQ
Biol. Unit 3
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (143 KB)
Biol.Unit 2 (142 KB)
Biol.Unit 3 (141 KB)
Biol.Unit 4 (144 KB)
Biol.Unit 5 (140 KB)
Biol.Unit 6 (137 KB)
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Models
(2 )
Title
:
STRUCTURE OF THE READY 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
:
04 Feb 05 (Deposition) - 19 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,F,G,H,I,J,K,M,N (2 x)
Biol. Unit 1: A,H (1x)
Biol. Unit 2: B,I (1x)
Biol. Unit 3: C,J (1x)
Biol. Unit 4: D,K (1x)
Biol. Unit 5: F,M (1x)
Biol. Unit 6: G,N (1x)
Keywords
:
Nib State, Hydroxide Bridge, 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
)
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
1c: FE3-S4 CLUSTER (F3Sc)
1d: FE3-S4 CLUSTER (F3Sd)
1e: FE3-S4 CLUSTER (F3Se)
1f: FE3-S4 CLUSTER (F3Sf)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
2b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
2c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
2d: CARBONMONOXIDE-(DICYANO) IRON (FCOd)
2e: CARBONMONOXIDE-(DICYANO) IRON (FCOe)
2f: CARBONMONOXIDE-(DICYANO) IRON (FCOf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
4c: NICKEL (II) ION (NIc)
4d: NICKEL (II) ION (NId)
4e: NICKEL (II) ION (NIe)
4f: NICKEL (II) ION (NIf)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
5c: IRON/SULFUR CLUSTER (SF4c)
5d: IRON/SULFUR CLUSTER (SF4d)
5e: IRON/SULFUR CLUSTER (SF4e)
5f: IRON/SULFUR CLUSTER (SF4f)
5g: IRON/SULFUR CLUSTER (SF4g)
5h: IRON/SULFUR CLUSTER (SF4h)
5i: IRON/SULFUR CLUSTER (SF4i)
5j: IRON/SULFUR CLUSTER (SF4j)
5k: IRON/SULFUR CLUSTER (SF4k)
5l: IRON/SULFUR CLUSTER (SF4l)
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
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NI
-1
Ligand/Ion
NICKEL (II) ION
5
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(6, 6)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC9 (SOFTWARE)
3: CC3 (SOFTWARE)
4: CC4 (SOFTWARE)
5: CC5 (SOFTWARE)
6: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
CYS J:72 , CYS J:75 , CYS J:543 , CYS J:546 , FCO J:550 , HOH J:557
BINDING SITE FOR RESIDUE NI J 551
2
AC9
SOFTWARE
GLU J:53 , LEU J:495 , HIS J:549 , HOH J:554 , HOH J:555 , HOH J:556
BINDING SITE FOR RESIDUE MG J 553
3
CC3
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
CC4
SOFTWARE
THR C:223 , ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , GLN J:230
BINDING SITE FOR RESIDUE F3S C 266
5
CC5
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , GLY C:112 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , PRO C:148 , ARG J:70 , HIS J:228
BINDING SITE FOR RESIDUE SF4 C 267
6
CC6
SOFTWARE
CYS J:75 , VAL J:78 , HIS J:79 , ALA J:474 , PRO J:475 , ARG J:476 , LEU J:479 , VAL J:497 , PRO J:498 , SER J:499 , CYS J:546 , NI J:551 , HOH J:557
BINDING SITE FOR RESIDUE FCO J 550
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (J:50-75)
2: NI_HGENASE_L_2 (J:540-549)
;
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_DESFR
50-75
1
-
-
J:50-75
-
-
-
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
1
-
-
J:540-549
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1yrqa_ (A:)
1b: SCOP_d1yrqb_ (B:)
1c: SCOP_d1yrqc_ (C:)
1d: SCOP_d1yrqd_ (D:)
1e: SCOP_d1yrqf_ (F:)
1f: SCOP_d1yrqg_ (G:)
2a: SCOP_d1yrqh_ (H:)
2b: SCOP_d1yrqi_ (I:)
2c: SCOP_d1yrqj_ (J:)
2d: SCOP_d1yrqk_ (K:)
2e: SCOP_d1yrqm_ (M:)
2f: SCOP_d1yrqn_ (N:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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 fructosovorans [TaxId: 878]
(5)
1a
d1yrqa_
A:
1b
d1yrqb_
B:
1c
d1yrqc_
C:
1d
d1yrqd_
D:
1e
d1yrqf_
F:
1f
d1yrqg_
G:
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
d1yrqh_
H:
2b
d1yrqi_
I:
2c
d1yrqj_
J:
2d
d1yrqk_
K:
2e
d1yrqm_
M:
2f
d1yrqn_
N:
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_1yrqA01 (A:3-178)
1b: CATH_1yrqB01 (B:3-178)
1c: CATH_1yrqD01 (D:3-178)
1d: CATH_1yrqG01 (G:3-178)
1e: CATH_1yrqC01 (C:5-178)
1f: CATH_1yrqF01 (F:5-178)
2a: CATH_1yrqA02 (A:179-263)
2b: CATH_1yrqB02 (B:179-263)
2c: CATH_1yrqC02 (C:179-263)
2d: CATH_1yrqD02 (D:179-263)
2e: CATH_1yrqF02 (F:179-263)
2f: CATH_1yrqG02 (G:179-263)
3a: CATH_1yrqJ00 (J:6-549)
3b: CATH_1yrqK00 (K:6-549)
3c: CATH_1yrqH00 (H:5-549)
3d: CATH_1yrqI00 (I:5-549)
3e: CATH_1yrqM00 (M:5-549)
3f: CATH_1yrqN00 (N:5-549)
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 fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
1a
1yrqA01
A:3-178
1b
1yrqB01
B:3-178
1c
1yrqD01
D:3-178
1d
1yrqG01
G:3-178
1e
1yrqC01
C:5-178
1f
1yrqF01
F: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
1yrqA02
A:179-263
2b
1yrqB02
B:179-263
2c
1yrqC02
C:179-263
2d
1yrqD02
D:179-263
2e
1yrqF02
F:179-263
2f
1yrqG02
G: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
1yrqJ00
J:6-549
3b
1yrqK00
K:6-549
3c
1yrqH00
H:5-549
3d
1yrqI00
I:5-549
3e
1yrqM00
M:5-549
3f
1yrqN00
N:5-549
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_1yrqN01 (N:50-549)
1b: PFAM_NiFeSe_Hases_1yrqN02 (N:50-549)
1c: PFAM_NiFeSe_Hases_1yrqN03 (N:50-549)
1d: PFAM_NiFeSe_Hases_1yrqN04 (N:50-549)
1e: PFAM_NiFeSe_Hases_1yrqN05 (N:50-549)
1f: PFAM_NiFeSe_Hases_1yrqN06 (N:50-549)
2a: PFAM_Oxidored_q6_1yrqG01 (G:17-161)
2b: PFAM_Oxidored_q6_1yrqG02 (G:17-161)
2c: PFAM_Oxidored_q6_1yrqG03 (G:17-161)
2d: PFAM_Oxidored_q6_1yrqG04 (G:17-161)
2e: PFAM_Oxidored_q6_1yrqG05 (G:17-161)
2f: PFAM_Oxidored_q6_1yrqG06 (G:17-161)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Desulfovibrio fructosovorans
(2)
1a
NiFeSe_Hases-1yrqN01
N:50-549
1b
NiFeSe_Hases-1yrqN02
N:50-549
1c
NiFeSe_Hases-1yrqN03
N:50-549
1d
NiFeSe_Hases-1yrqN04
N:50-549
1e
NiFeSe_Hases-1yrqN05
N:50-549
1f
NiFeSe_Hases-1yrqN06
N:50-549
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Desulfovibrio fructosovorans
(2)
2a
Oxidored_q6-1yrqG01
G:17-161
2b
Oxidored_q6-1yrqG02
G:17-161
2c
Oxidored_q6-1yrqG03
G:17-161
2d
Oxidored_q6-1yrqG04
G:17-161
2e
Oxidored_q6-1yrqG05
G:17-161
2f
Oxidored_q6-1yrqG06
G:17-161
[
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Asymmetric Unit 1
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Asym.Unit (1.5 MB)
Header - Asym.Unit
Biol.Unit 1 (143 KB)
Header - Biol.Unit 1
Biol.Unit 2 (142 KB)
Header - Biol.Unit 2
Biol.Unit 3 (141 KB)
Header - Biol.Unit 3
Biol.Unit 4 (144 KB)
Header - Biol.Unit 4
Biol.Unit 5 (140 KB)
Header - Biol.Unit 5
Biol.Unit 6 (137 KB)
Header - Biol.Unit 6
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