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2WPN
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (127 KB)
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(1)
Title
:
STRUCTURE OF THE OXIDISED, AS-ISOLATED NIFESE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH
Authors
:
M. C. Marques, R. Coelho, A. L. Delacey, I. A. C. Pereira, P. M. Matias
Date
:
07 Aug 09 (Deposition) - 12 Jan 10 (Release) - 05 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.04
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrogenase, Metal-Binding, Oxidoreductase, Oxygen Tolerance
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Marques, R. Coelho, A. L. De Lacey, I. A. C. Pereira, P. M. Matias
The Three-Dimensional Structure Of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough: A Hydrogenase Without A Bridging Ligand In The Active Site In Its Oxidised, "As- Isolated" State.
J. Mol. Biol. V. 396 893 2010
(for further references see the
PDB file header
)
[
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Hetero Components
(9, 14)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3a: FE (II) ION (FE2a)
4a: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BI... (FSXa)
5a: NICKEL (II) ION (NIa)
6a: CYSTEINESULFONIC ACID (OCSa)
7a: 3-(SULFANYLSELANYL)-L-ALANINE (PSWa)
8a: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYa)
8b: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYb)
8c: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYc)
8d: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYd)
9a: IRON/SULFUR CLUSTER (SF4a)
9b: IRON/SULFUR CLUSTER (SF4b)
9c: IRON/SULFUR CLUSTER (SF4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
3
FE2
1
Ligand/Ion
FE (II) ION
4
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)
5
NI
1
Ligand/Ion
NICKEL (II) ION
6
OCS
1
Mod. Amino Acid
CYSTEINESULFONIC ACID
7
PSW
1
Mod. Amino Acid
3-(SULFANYLSELANYL)-L-ALANINE
8
SBY
4
Ligand/Ion
3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
9
SF4
3
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , TYR A:217 , CYS A:232 , ARG A:233 , TYR A:234 , CYS A:238 , GLY A:240 , VAL A:260
BINDING SITE FOR RESIDUE SF4 A1284
02
AC2
SOFTWARE
THR A:243 , CYS A:247 , TRP A:252 , CYS A:259 , CYS A:265 , ILE A:266 , CYS A:268 , ARG B:182 , GLN B:187
BINDING SITE FOR RESIDUE SF4 A1285
03
AC3
SOFTWARE
CYS A:18 , THR A:19 , GLY A:20 , CYS A:21 , GLU A:77 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , HOH A:2031 , HIS B:185
BINDING SITE FOR RESIDUE FSX A1287
04
AC4
SOFTWARE
GLY A:17 , CYS A:18 , CYS A:21 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , ARG B:73 , HIS B:185
BINDING SITE FOR RESIDUE SF4 A1286
05
AC5
SOFTWARE
SER A:22 , LEU A:37 , GLU B:167
BINDING SITE FOR RESIDUE SBY A1288
06
AC6
SOFTWARE
PHE A:73 , VAL A:170
BINDING SITE FOR RESIDUE SBY A1289
07
AC7
SOFTWARE
CYS B:78 , HIS B:82 , ALA B:420 , PRO B:421 , ARG B:422 , LEU B:425 , ALA B:444 , SER B:445 , PSW B:489 , CYS B:492 , NI B:1498
BINDING SITE FOR RESIDUE FCO B1497
08
AC8
SOFTWARE
OCS B:75 , CYS B:78 , SEC B:489 , PSW B:489 , CYS B:492 , FCO B:1497
BINDING SITE FOR RESIDUE NI B1498
09
AC9
SOFTWARE
GLU B:56 , ILE B:441 , HIS B:495 , HOH B:2031 , HOH B:2119 , HOH B:2120
BINDING SITE FOR RESIDUE FE2 B1499
10
BC1
SOFTWARE
CYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421
BINDING SITE FOR RESIDUE CL B1500
11
BC2
SOFTWARE
GLN B:128 , VAL B:131 , PRO B:134 , PHE B:139 , TYR B:162
BINDING SITE FOR RESIDUE SBY B1501
12
BC3
SOFTWARE
TYR B:162
BINDING SITE FOR RESIDUE SBY B1502
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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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.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2wpna_ (A:)
2a: SCOP_d2wpnb_ (B:)
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Classes
(
)
(
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(
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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 vulgaris [TaxId: 882]
(6)
1a
d2wpna_
A:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfovibrio vulgaris [TaxId: 882]
(6)
2a
d2wpnb_
B:
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2wpnA01 (A:7-202)
2a: CATH_2wpnA02 (A:203-283)
3a: CATH_2wpnB00 (B:15-495)
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Topologies
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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 vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
1a
2wpnA01
A:7-202
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 vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
2a
2wpnA02
A:203-283
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
3a
2wpnB00
B:15-495
[
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]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_2wpnB01 (B:141-495)
1b: PFAM_NiFeSe_Hases_2wpnB02 (B:141-495)
2a: PFAM_Oxidored_q6_2wpnA01 (A:18-173)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
1a
NiFeSe_Hases-2wpnB01
B:141-495
1b
NiFeSe_Hases-2wpnB02
B:141-495
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
2a
Oxidored_q6-2wpnA01
A:18-173
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