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2FRV
Biol. Unit 4
Info
Asym.Unit (759 KB)
Biol.Unit 1 (136 KB)
Biol.Unit 2 (135 KB)
Biol.Unit 3 (135 KB)
Biol.Unit 4 (136 KB)
Biol.Unit 5 (136 KB)
Biol.Unit 6 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Authors
:
A. Volbeda, M. Frey, J. C. Fontecilla-Camps
Date
:
10 Jun 97 (Deposition) - 17 Jun 98 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.54
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,L,S
Biol. Unit 1: L,S (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Biol. Unit 4: E,F (1x)
Biol. Unit 5: G,H (1x)
Biol. Unit 6: I,J (1x)
Keywords
:
Oxidoreductase, Ni-Fe Hydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, E. Garcin, C. Piras, A. L. De Lacey, V. M. Fernandez, E. C. Hatchikian, M. Frey, J. C. Fontecilla-Camps
Structure Of The [Nife] Hydrogenase Active Site: Evidence For Biologically Uncommon Fe Ligands
J. Am. Chem. Soc. V. 118 12989 1996
(for further references see the
PDB file header
)
[
close entry info
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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: OXYGEN ATOM (Oa)
5b: OXYGEN ATOM (Ob)
5c: OXYGEN ATOM (Oc)
5d: OXYGEN ATOM (Od)
5e: OXYGEN ATOM (Oe)
5f: OXYGEN ATOM (Of)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
6i: IRON/SULFUR CLUSTER (SF4i)
6j: IRON/SULFUR CLUSTER (SF4j)
6k: IRON/SULFUR CLUSTER (SF4k)
6l: 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
O
-1
Ligand/Ion
OXYGEN ATOM
6
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC4 (SOFTWARE)
2: BC1 (SOFTWARE)
3: DC1 (SOFTWARE)
4: DC2 (SOFTWARE)
5: DC3 (SOFTWARE)
6: DC4 (SOFTWARE)
7: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
CYS F:65 , CYS F:68 , CYS F:530 , CYS F:533 , FCO F:537 , O F:539
BINDING SITE FOR RESIDUE NI F 538
2
BC1
SOFTWARE
GLU F:46 , LEU F:482 , HIS F:536 , HOH F:5050 , HOH F:5051 , HOH F:5052
BINDING SITE FOR RESIDUE MG F 540
3
DC1
SOFTWARE
HIS E:185 , CYS E:188 , CYS E:213 , LEU E:214 , CYS E:219
BINDING SITE FOR RESIDUE SF4 E 265
4
DC2
SOFTWARE
THR E:224 , ASN E:226 , CYS E:228 , PHE E:233 , TRP E:238 , PRO E:239 , CYS E:246 , ILE E:247 , CYS E:249 , LYS F:216 , GLN F:221
BINDING SITE FOR RESIDUE F3S E 266
5
DC3
SOFTWARE
GLU E:16 , CYS E:17 , CYS E:20 , GLY E:110 , THR E:111 , CYS E:112 , GLY E:147 , CYS E:148 , PRO E:149 , ARG F:63 , HIS F:219
BINDING SITE FOR RESIDUE SF4 E 267
6
DC4
SOFTWARE
CYS F:68 , VAL F:71 , HIS F:72 , ALA F:461 , PRO F:462 , ARG F:463 , LEU F:466 , VAL F:484 , PRO F:485 , SER F:486 , CYS F:533 , NI F:538 , O F:539
BINDING SITE FOR RESIDUE FCO F 537
7
DC5
SOFTWARE
CYS F:68 , ARG F:463 , CYS F:530 , CYS F:533 , FCO F:537 , NI F:538
BINDING SITE FOR RESIDUE O F 539
[
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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 (F:43-68)
2: NI_HGENASE_L_2 (F: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
-
-
F:43-68
-
-
-
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESGI
527-536
1
-
-
F:527-536
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d2frva_ (A:)
1b: SCOP_d2frvc_ (C:)
1c: SCOP_d2frve_ (E:)
1d: SCOP_d2frvg_ (G:)
1e: SCOP_d2frvi_ (I:)
1f: SCOP_d2frvs_ (S:)
2a: SCOP_d2frvb_ (B:)
2b: SCOP_d2frvd_ (D:)
2c: SCOP_d2frvf_ (F:)
2d: SCOP_d2frvh_ (H:)
2e: SCOP_d2frvj_ (J:)
2f: SCOP_d2frvl_ (L:)
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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
:
Nickel-iron hydrogenase, small subunit
(16)
Desulfovibrio gigas [TaxId: 879]
(2)
1a
d2frva_
A:
1b
d2frvc_
C:
1c
d2frve_
E:
1d
d2frvg_
G:
1e
d2frvi_
I:
1f
d2frvs_
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 gigas [TaxId: 879]
(3)
2a
d2frvb_
B:
2b
d2frvd_
D:
2c
d2frvf_
F:
2d
d2frvh_
H:
2e
d2frvj_
J:
2f
d2frvl_
L:
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_2frvA01 (A:4-179)
1b: CATH_2frvC01 (C:4-179)
1c: CATH_2frvE01 (E:4-179)
1d: CATH_2frvG01 (G:4-179)
1e: CATH_2frvI01 (I:4-179)
1f: CATH_2frvS01 (S:4-179)
2a: CATH_2frvA02 (A:180-264)
2b: CATH_2frvC02 (C:180-264)
2c: CATH_2frvE02 (E:180-264)
2d: CATH_2frvG02 (G:180-264)
2e: CATH_2frvI02 (I:180-264)
2f: CATH_2frvS02 (S:180-264)
3a: CATH_2frvB00 (B:7-536)
3b: CATH_2frvD00 (D:7-536)
3c: CATH_2frvF00 (F:7-536)
3d: CATH_2frvH00 (H:7-536)
3e: CATH_2frvJ00 (J:7-536)
3f: CATH_2frvL00 (L:7-536)
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)
(
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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.
(2)
1a
2frvA01
A:4-179
1b
2frvC01
C:4-179
1c
2frvE01
E:4-179
1d
2frvG01
G:4-179
1e
2frvI01
I:4-179
1f
2frvS01
S:4-179
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.
(2)
2a
2frvA02
A:180-264
2b
2frvC02
C:180-264
2c
2frvE02
E:180-264
2d
2frvG02
G:180-264
2e
2frvI02
I:180-264
2f
2frvS02
S: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.
(2)
3a
2frvB00
B:7-536
3b
2frvD00
D:7-536
3c
2frvF00
F:7-536
3d
2frvH00
H:7-536
3e
2frvJ00
J:7-536
3f
2frvL00
L:7-536
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Asym.Unit (759 KB)
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Biol.Unit 3 (135 KB)
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Biol.Unit 4 (136 KB)
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