PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1HFE
Asym. Unit
Info
Asym.Unit (191 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (94 KB)
Biol.Unit 3 (183 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
Authors
:
Y. Nicolet, C. Piras, P. Legrand, E. C. Hatchikian, J. C. Fontecilla- Camps
Date
:
11 Nov 98 (Deposition) - 20 Apr 99 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : L,M,S,T
Biol. Unit 1: L,S (1x)
Biol. Unit 2: M,T (1x)
Biol. Unit 3: L,M,S,T (1x)
Keywords
:
Fe-Only Hydrogenase, Hydrogene Metabolism, Periplasm, Hydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Nicolet, C. Piras, P. Legrand, C. E. Hatchikian, J. C. Fontecilla-Camps
Desulfovibrio Desulfuricans Iron Hydrogenase: The Structure Shows Unusual Coordination To An Active Site Fe Binuclear Center.
Structure Fold. Des. V. 7 13 1999
[
close entry info
]
Hetero Components
(7, 23)
Info
All Hetero Components
1a: CARBON MONOXIDE (CMOa)
1b: CARBON MONOXIDE (CMOb)
1c: CARBON MONOXIDE (CMOc)
1d: CARBON MONOXIDE (CMOd)
2a: CYANIDE ION (CYNa)
2b: CYANIDE ION (CYNb)
2c: CYANIDE ION (CYNc)
2d: CYANIDE ION (CYNd)
3a: CYSTEINE (CYSa)
3b: CYSTEINE (CYSb)
4a: FE (II) ION (FE2a)
4b: FE (II) ION (FE2b)
4c: FE (II) ION (FE2c)
4d: FE (II) ION (FE2d)
5a: 1,3-PROPANEDITHIOL (PDTa)
5b: 1,3-PROPANEDITHIOL (PDTb)
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)
7a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CMO
4
Ligand/Ion
CARBON MONOXIDE
2
CYN
4
Ligand/Ion
CYANIDE ION
3
CYS
2
Mod. Amino Acid
CYSTEINE
4
FE2
4
Ligand/Ion
FE (II) ION
5
PDT
2
Ligand/Ion
1,3-PROPANEDITHIOL
6
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
7
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS L:382 , PDT L:425 , FE2 L:427 , CYN L:429 , CMO L:430 , HOH L:433
BINDING SITE FOR RESIDUE FE2 L 426
02
AC2
SOFTWARE
PDT L:425 , FE2 L:426 , CYN L:428 , CYN L:429 , CMO L:431 , HOH L:433
BINDING SITE FOR RESIDUE FE2 L 427
03
AC3
SOFTWARE
PRO L:203 , ILE L:204 , LYS L:237 , PDT L:425 , FE2 L:427 , CMO L:431 , HOH L:433
BINDING SITE FOR RESIDUE CYN L 428
04
AC4
SOFTWARE
ALA L:107 , PRO L:108 , ALA L:109 , CYS L:382 , PDT L:425 , FE2 L:426 , FE2 L:427 , CMO L:430 , HOH L:433
BINDING SITE FOR RESIDUE CYN L 429
05
AC5
SOFTWARE
CYS M:382 , PDT M:425 , FE2 M:427 , CYN M:429 , CMO M:430 , HOH M:434
BINDING SITE FOR RESIDUE FE2 M 426
06
AC6
SOFTWARE
PDT M:425 , FE2 M:426 , CYN M:428 , CYN M:429 , CMO M:431 , HOH M:434
BINDING SITE FOR RESIDUE FE2 M 427
07
AC7
SOFTWARE
PRO M:203 , ILE M:204 , LYS M:237 , PDT M:425 , FE2 M:427 , CMO M:431 , HOH M:434
BINDING SITE FOR RESIDUE CYN M 428
08
AC8
SOFTWARE
ALA M:107 , PRO M:108 , ALA M:109 , CYS M:382 , PDT M:425 , FE2 M:426 , FE2 M:427 , CMO M:430
BINDING SITE FOR RESIDUE CYN M 429
09
AC9
SOFTWARE
HIS S:82 , ASP S:86 , HIS T:82 , ASP T:86
BINDING SITE FOR RESIDUE ZN S 500
10
BC1
SOFTWARE
CYS L:35 , ILE L:36 , GLY L:37 , CYS L:38 , ASP L:39 , CYS L:41 , HIS L:58 , CYS L:76 , GLU L:78 , ILE L:81
BINDING SITE FOR RESIDUE SF4 L 422
11
BC2
SOFTWARE
VAL L:28 , CYS L:45 , ILE L:50 , ILE L:60 , CYS L:66 , ILE L:67 , CYS L:69 , GLY L:70 , CYS L:72
BINDING SITE FOR RESIDUE SF4 L 423
12
BC3
SOFTWARE
CYS L:179 , PRO L:180 , CYS L:234 , ALA L:377 , CYS L:378 , CYS L:382 , GLY L:385 , PDT L:425
BINDING SITE FOR RESIDUE SF4 L 424
13
BC4
SOFTWARE
CYS L:178 , LYS L:237 , PHE L:296 , MET L:376 , CYS L:382 , SF4 L:424 , FE2 L:426 , FE2 L:427 , CYN L:428 , CYN L:429 , CMO L:430 , CMO L:431
BINDING SITE FOR RESIDUE PDT L 425
14
BC5
SOFTWARE
MET L:232 , PRO L:233 , CYS L:234 , LYS L:237 , CYS L:382 , PDT L:425 , FE2 L:426 , CYN L:429 , HOH L:433
BINDING SITE FOR RESIDUE CMO L 430
15
BC6
SOFTWARE
PRO L:108 , ALA L:149 , PRO L:203 , PHE L:296 , PDT L:425 , FE2 L:427 , CYN L:428 , HOH L:433
BINDING SITE FOR RESIDUE CMO L 431
16
BC7
SOFTWARE
CYS M:35 , ILE M:36 , GLY M:37 , CYS M:38 , ASP M:39 , CYS M:41 , HIS M:58 , CYS M:76 , GLU M:78 , ILE M:81
BINDING SITE FOR RESIDUE SF4 M 422
17
BC8
SOFTWARE
CYS M:45 , ILE M:50 , ILE M:60 , CYS M:66 , ILE M:67 , CYS M:69 , GLY M:70 , CYS M:72
BINDING SITE FOR RESIDUE SF4 M 423
18
BC9
SOFTWARE
CYS M:179 , PRO M:180 , CYS M:234 , ALA M:377 , CYS M:378 , CYS M:382 , GLY M:385 , PDT M:425
BINDING SITE FOR RESIDUE SF4 M 424
19
CC1
SOFTWARE
CYS M:178 , LYS M:237 , PHE M:296 , MET M:376 , CYS M:382 , SF4 M:424 , FE2 M:426 , FE2 M:427 , CYN M:428 , CYN M:429 , CMO M:430 , CMO M:431
BINDING SITE FOR RESIDUE PDT M 425
20
CC2
SOFTWARE
MET M:232 , PRO M:233 , CYS M:234 , LYS M:237 , CYS M:382 , PDT M:425 , FE2 M:426 , CYN M:429 , HOH M:434
BINDING SITE FOR RESIDUE CMO M 430
21
CC3
SOFTWARE
PRO M:108 , ALA M:149 , PRO M:203 , PHE M:296 , PDT M:425 , FE2 M:427 , CYN M:428 , HOH M:434
BINDING SITE FOR RESIDUE CMO M 431
22
CC4
SOFTWARE
THR L:74 , CYS L:384 , GLY L:385 , GLN L:388 , PRO L:389 , VAL L:390 , MET L:391 , ARG S:46
BINDING SITE FOR RESIDUE CYS L 432
23
CC5
SOFTWARE
THR M:74 , CYS M:384 , GLY M:385 , GLN M:388 , PRO M:389 , VAL M:390 , MET M:391 , ARG T:46
BINDING SITE FOR RESIDUE CYS M 433
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (L:26-57,M:26-57|L:59-86,M:59-86)
2: 4FE4S_FER_1 (L:35-46,M:35-46|L:66-77,M:66-77)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
PHFL_DESVH
26-57
59-86
4
L:26-57
M:26-57
L:59-86
M:59-86
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
PHFL_DESVH
35-46
66-77
4
L:35-46
M:35-46
L:66-77
M:66-77
[
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.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1hfes_ (S:)
1b: SCOP_d1hfet_ (T:)
2a: SCOP_d1hfel2 (L:2-86)
2b: SCOP_d1hfem2 (M:2-86)
3a: SCOP_d1hfel1 (L:87-398)
3b: SCOP_d1hfem1 (M:87-398)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Non-globular all-alpha subunits of globular proteins
(135)
Superfamily
:
Fe-only hydrogenase smaller subunit
(1)
Family
:
Fe-only hydrogenase smaller subunit
(1)
Protein domain
:
Fe-only hydrogenase smaller subunit
(1)
Desulfovibrio desulfuricans [TaxId: 876]
(1)
1a
d1hfes_
S:
1b
d1hfet_
T:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Fe-only hydrogenase larger subunit, N-domain
(1)
Desulfovibrio desulfuricans [TaxId: 876]
(1)
2a
d1hfel2
L:2-86
2b
d1hfem2
M:2-86
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Fe-only hydrogenase
(5)
Superfamily
:
Fe-only hydrogenase
(5)
Family
:
Fe-only hydrogenase
(5)
Protein domain
:
Fe-only hydrogenase larger subunit, C-domain
(1)
Desulfovibrio desulfuricans [TaxId: 876]
(1)
3a
d1hfel1
L:87-398
3b
d1hfem1
M:87-398
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1hfeL02 (L:30-81)
1b: CATH_1hfeM02 (M:30-81)
2a: CATH_1hfeL03 (L:149-200,L:290-380)
2b: CATH_1hfeM03 (M:149-200,M:290-380)
3a: CATH_1hfeL01 (L:2-29,L:82-148,L:201-289,L:381-397)
3b: CATH_1hfeM01 (M:2-29,M:82-148,M:201-289,M:381-397)
4a: CATH_1hfeS00 (S:36-123)
4b: CATH_1hfeT00 (T:36-123)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.20, no name defined]
(120)
Vulgaris str (Desulfovibrio vulgaris subsp)
(1)
1a
1hfeL02
L:30-81
1b
1hfeM02
M:30-81
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
(1)
Homologous Superfamily
:
Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
(1)
Vulgaris str (Desulfovibrio vulgaris subsp)
(1)
2a
1hfeL03
L:149-200,L:290-380
2b
1hfeM03
M:149-200,M:290-380
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1780, no name defined]
(1)
Vulgaris str (Desulfovibrio vulgaris subsp)
(1)
3a
1hfeL01
L:2-29,L:82-148,L:201-289,L:381-397
3b
1hfeM01
M:2-29,M:82-148,M:201-289,M:381-397
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
G Protein Gi Gamma 2
(12)
Homologous Superfamily
:
[code=4.10.260.20, no name defined]
(1)
Vulgaris str (Desulfovibrio vulgaris subsp)
(1)
4a
1hfeS00
S:36-123
4b
1hfeT00
T:36-123
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain L
Chain M
Chain S
Chain T
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (191 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
Biol.Unit 2 (94 KB)
Header - Biol.Unit 2
Biol.Unit 3 (183 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1HFE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help