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1E3D
Biol. Unit 1
Info
Asym.Unit (515 KB)
Biol.Unit 1 (258 KB)
Biol.Unit 2 (256 KB)
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(1)
Title
:
[NIFE] HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
Authors
:
P. M. Matias, C. M. Soares, L. M. Saraiva, R. Coelho, J. Morais, J. Le Gall, M. A. Carrondo
Date
:
14 Jun 00 (Deposition) - 14 Jun 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Hydrogenase, Crystal Structure, Molecular Modelling, Electron Transfer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. M. Matias, C. M. Soares, L. M. Saraiva, R. Coelho, J. Morais, J. Le Gall, M. A. Carrondo
[Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination And Refinement At 1. 8 A And Modelling Studies Of Its Interaction With The Tetrahaem Cytochrome C3.
J. Biol. Inorg. Chem. V. 6 63 2001
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICA... (FNEa)
2b: (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICA... (FNEb)
3a: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BI... (FSXa)
3b: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BI... (FSXb)
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: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
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
FSX
1
Ligand/Ion
BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
4
H2S
2
Ligand/Ion
HYDROSULFURIC ACID
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU B:52 , LEU B:488 , HIS B:542 , HOH B:2070 , HOH B:2355 , HOH B:2358
BINDING SITE FOR RESIDUE MG B 901
2
AC3
SOFTWARE
ASN A:228 , CYS A:230 , PHE A:235 , TRP A:240 , PRO A:241 , CYS A:248 , ILE A:249 , CYS A:251 , LYS B:222 , GLN B:227
BINDING SITE FOR RESIDUE F3S A 267
3
AC4
SOFTWARE
HIS A:187 , CYS A:190 , ARG A:192 , ARG A:193 , CYS A:215 , LEU A:216 , CYS A:221
BINDING SITE FOR RESIDUE SF4 A 268
4
AC5
SOFTWARE
GLU A:16 , CYS A:17 , THR A:18 , GLY A:19 , CYS A:20 , GLU A:75 , THR A:113 , CYS A:114 , GLY A:149 , CYS A:150 , PRO A:151 , HOH A:2122 , HIS B:225
BINDING SITE FOR RESIDUE FSX A 269
5
AC6
SOFTWARE
CYS B:71 , CYS B:74 , HIS B:78 , VAL B:467 , SER B:468 , ARG B:469 , LEU B:472 , VAL B:490 , PRO B:491 , THR B:492 , CYS B:536 , CYS B:539
BINDING SITE FOR RESIDUE FNE B 543
6
BC2
SOFTWARE
GLY A:119 , ASN A:255 , HOH A:2124
BINDING SITE FOR RESIDUE H2S A 904
7
BC5
SOFTWARE
LEU B:106 , PHE B:110 , VAL B:467 , SER B:468
BINDING SITE FOR RESIDUE H2S B 904
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1e3da_ (A:)
1b: SCOP_d1e3dc_ (C:)
2a: SCOP_d1e3db_ (B:)
2b: SCOP_d1e3dd_ (D:)
View:
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Classes
(
)
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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 desulfuricans [TaxId: 876]
(1)
1a
d1e3da_
A:
1b
d1e3dc_
C:
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 desulfuricans [TaxId: 876]
(1)
2a
d1e3db_
B:
2b
d1e3dd_
D:
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1e3dA01 (A:5-181)
1b: CATH_1e3dC01 (C:5-181)
2a: CATH_1e3dA02 (A:182-266)
2b: CATH_1e3dC02 (C:182-266)
3a: CATH_1e3dB00 (B:6-542)
3b: CATH_1e3dD00 (D:6-542)
View:
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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 desulfuricans. Organism_taxid: 876.
(1)
1a
1e3dA01
A:5-181
1b
1e3dC01
C:5-181
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 desulfuricans. Organism_taxid: 876.
(1)
2a
1e3dA02
A:182-266
2b
1e3dC02
C:182-266
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(1)
3a
1e3dB00
B:6-542
3b
1e3dD00
D:6-542
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Asym.Unit (515 KB)
Header - Asym.Unit
Biol.Unit 1 (258 KB)
Header - Biol.Unit 1
Biol.Unit 2 (256 KB)
Header - Biol.Unit 2
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