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Biol. Unit 3
Info
Asym.Unit (425 KB)
Biol.Unit 1 (146 KB)
Biol.Unit 2 (145 KB)
Biol.Unit 3 (141 KB)
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(1)
Title
:
STRUCTURE OF THE OXIDIZED UNREADY FORM OF NI-FE HYDROGENASE
Authors
:
A. Volbeda
Date
:
02 Feb 05 (Deposition) - 19 Apr 05 (Release) - 31 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.83
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: B,R (1x)
Biol. Unit 3: C,S (1x)
Keywords
:
Ni-Fe Hydrogenase Unready State, 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
(6, 9)
Info
All Hetero Components
1a: BICARBONATE ION (BCTa)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
3a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
4a: FE (II) ION (FE2a)
4b: FE (II) ION (FE2b)
4c: FE (II) ION (FE2c)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
5f: GLYCEROL (GOLf)
5g: GLYCEROL (GOLg)
5h: GLYCEROL (GOLh)
5i: GLYCEROL (GOLi)
5j: GLYCEROL (GOLj)
5k: GLYCEROL (GOLk)
5l: GLYCEROL (GOLl)
5m: GLYCEROL (GOLm)
5n: GLYCEROL (GOLn)
5o: GLYCEROL (GOLo)
5p: GLYCEROL (GOLp)
5q: GLYCEROL (GOLq)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
7a: NICKEL (II) ION (NIa)
7b: NICKEL (II) ION (NIb)
7c: NICKEL (II) ION (NIc)
8a: PEROXIDE ION (PERa)
8b: PEROXIDE ION (PERb)
8c: PEROXIDE ION (PERc)
9a: IRON/SULFUR CLUSTER (SF4a)
9b: IRON/SULFUR CLUSTER (SF4b)
9c: IRON/SULFUR CLUSTER (SF4c)
9d: IRON/SULFUR CLUSTER (SF4d)
9e: IRON/SULFUR CLUSTER (SF4e)
9f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCT
-1
Ligand/Ion
BICARBONATE ION
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
FE2
1
Ligand/Ion
FE (II) ION
5
GOL
3
Ligand/Ion
GLYCEROL
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
NI
-1
Ligand/Ion
NICKEL (II) ION
8
PER
1
Ligand/Ion
PEROXIDE ION
9
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AS3 (AUTHOR)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CT3 (AUTHOR)
11: DC3 (SOFTWARE)
12: EC2 (SOFTWARE)
13: EC4 (SOFTWARE)
14: EC5 (SOFTWARE)
15: EC6 (SOFTWARE)
16: FD3 (AUTHOR)
17: FM3 (AUTHOR)
18: FP3 (AUTHOR)
19: PO3 (AUTHOR)
20: SO3 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
CYS S:72 , CYS S:75 , CYS S:543 , CYS S:546 , FCO S:550 , PER S:552 , HOH S:557
BINDING SITE FOR RESIDUE NI S 551
02
AC6
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:554 , HOH S:555 , HOH S:556
BINDING SITE FOR RESIDUE FE2 S 553
03
AC8
SOFTWARE
HOH A:360 , HOH C:269 , HOH C:270 , ASN Q:181 , HOH Q:1026 , HOH Q:1031
BINDING SITE FOR RESIDUE MG Q 555
04
AS3
AUTHOR
CYS S:72 , CYS S:75 , CYS S:543 , CYS S:546 , FCO S:550 , NI S:551
NI-FE ACTIVE SITE IN MOLECULE 3 SITE
05
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
06
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 S:230
BINDING SITE FOR RESIDUE F3S C 266
07
CC5
SOFTWARE
CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , PRO C:148 , ARG S:70 , HIS S:228
BINDING SITE FOR RESIDUE SF4 C 267
08
CC6
SOFTWARE
CYS S:75 , VAL S:78 , HIS S:79 , ALA S:474 , PRO S:475 , ARG S:476 , LEU S:479 , VAL S:497 , PRO S:498 , ALA S:499 , CYS S:546 , NI S:551 , PER S:552 , HOH S:2477
BINDING SITE FOR RESIDUE FCO S 550
09
CC7
SOFTWARE
CYS S:72 , CYS S:75 , ARG S:476 , CYS S:543 , CYS S:546 , FCO S:550 , NI S:551 , HOH S:557
BINDING SITE FOR RESIDUE PER S 552
10
CT3
AUTHOR
GLU S:53 , LEU S:495 , HIS S:549 , FE2 S:553 , HOH S:554 , HOH S:555 , HOH S:556
C-TERMINAL METAL SITE IN MOLECULE 3
11
DC3
SOFTWARE
ALA A:55 , PHE C:198 , ASN Q:181 , ALA Q:182 , LEU Q:185 , ARG Q:529 , HOH Q:872 , HOH Q:1031
BINDING SITE FOR RESIDUE GOL Q 558
12
EC2
SOFTWARE
ARG R:152 , PRO R:153 , ASN R:155 , SER R:156 , HOH R:1444 , HOH R:1472 , ALA S:451 , GOL S:2302
BINDING SITE FOR RESIDUE GOL R 1306
13
EC4
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , THR S:297 , GLU S:445 , HOH S:2405 , HOH S:2581 , HOH S:2593
BINDING SITE FOR RESIDUE GOL S 2301
14
EC5
SOFTWARE
GOL R:1306 , GLY S:450 , ALA S:451 , LYS S:452 , ASP S:453 , ASN S:454 , HOH S:2544
BINDING SITE FOR RESIDUE GOL S 2302
15
EC6
SOFTWARE
VAL C:235 , SER S:217 , ASN S:250 , HOH S:2524
BINDING SITE FOR RESIDUE GOL S 2303
16
FD3
AUTHOR
HIS C:184 , CYS C:187 , CYS C:212 , CYS C:218 , SF4 C:265
DISTAL [4FE-4S] CLUSTER IN MOLECULE 3 SITE
17
FM3
AUTHOR
CYS C:227 , CYS C:245 , CYS C:248 , F3S C:266
[3FE-4S] CLUSTER IN MOLECULE 3 SITE
18
FP3
AUTHOR
CYS C:17 , CYS C:20 , CYS C:114 , CYS C:147 , SF4 C:267
PROXIMAL [4FE-4S] CLUSTER IN MOLECULE 3 SITE
19
PO3
AUTHOR
NI S:551 , FCO S:550 , PER S:552
ACTIVE SITE BOUND PEROXIDE IN MOLECULE 3 SITE
20
SO3
AUTHOR
CYS S:75 , NI S:551 , HOH S:557
NIFE-BOUND SULPHENIC ACID IN MOLECULE 3 SITE
[
close Site info
]
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 (S:50-75)
2: NI_HGENASE_L_2 (S: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
-
-
S:50-75
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
1
-
-
S:540-549
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1yqwa_ (A:)
1b: SCOP_d1yqwb_ (B:)
1c: SCOP_d1yqwc_ (C:)
2a: SCOP_d1yqwq_ (Q:)
2b: SCOP_d1yqwr_ (R:)
2c: SCOP_d1yqws_ (S:)
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
d1yqwa_
A:
1b
d1yqwb_
B:
1c
d1yqwc_
C:
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
d1yqwq_
Q:
2b
d1yqwr_
R:
2c
d1yqws_
S:
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_1yqwA01 (A:3-178)
1b: CATH_1yqwB01 (B:3-178)
1c: CATH_1yqwC01 (C:5-178)
2a: CATH_1yqwA02 (A:179-263)
2b: CATH_1yqwB02 (B:179-263)
2c: CATH_1yqwC02 (C:179-263)
3a: CATH_1yqwQ00 (Q:6-549)
3b: CATH_1yqwS00 (S:6-549)
3c: CATH_1yqwR00 (R:5-549)
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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
1yqwA01
A:3-178
1b
1yqwB01
B:3-178
1c
1yqwC01
C: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
1yqwA02
A:179-263
2b
1yqwB02
B:179-263
2c
1yqwC02
C: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
1yqwQ00
Q:6-549
3b
1yqwS00
S:6-549
3c
1yqwR00
R:5-549
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_1yqwS01 (S:50-549)
1b: PFAM_NiFeSe_Hases_1yqwS02 (S:50-549)
1c: PFAM_NiFeSe_Hases_1yqwS03 (S:50-549)
2a: PFAM_Oxidored_q6_1yqwC01 (C:17-161)
2b: PFAM_Oxidored_q6_1yqwC02 (C:17-161)
2c: PFAM_Oxidored_q6_1yqwC03 (C:17-161)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Desulfovibrio fructosovorans
(2)
1a
NiFeSe_Hases-1yqwS01
S:50-549
1b
NiFeSe_Hases-1yqwS02
S:50-549
1c
NiFeSe_Hases-1yqwS03
S:50-549
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Desulfovibrio fructosovorans
(2)
2a
Oxidored_q6-1yqwC01
C:17-161
2b
Oxidored_q6-1yqwC02
C:17-161
2c
Oxidored_q6-1yqwC03
C:17-161
[
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]
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Asym.Unit (425 KB)
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