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.
3ZE6
Asym. Unit
Info
Asym.Unit (265 KB)
Biol.Unit 1 (255 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
3D STRUCTURE OF THE NI-FE-SE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE AS-ISOLATED OXIDIZED STATE AT 1.50 ANGSTROMS
Authors
:
M. C. Marques, R. Coelho, I. A. C. Pereira, P. M. Matias
Date
:
03 Dec 12 (Deposition) - 12 Jun 13 (Release) - 05 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase, Hydrogenase Biohydrogen Oxygen Tolerance
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Marques, R. Coelho, I. A. C. Pereira, P. M. Matias
Redox State-Dependent Changes In The Crystal Structure Of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough
Int. J. Hydrogen Energy 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(11, 17)
Info
All Hetero Components
01a: CHLORIDE ION (CLa)
02a: S-MERCAPTOCYSTEINE (CSSa)
03a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
04a: FE (II) ION (FE2a)
05a: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BI... (FSXa)
06a: GLYCEROL (GOLa)
07a: NICKEL (II) ION (NIa)
08a: CYSTEINESULFONIC ACID (OCSa)
09a: 3-(SULFANYLSELANYL)-L-ALANINE (PSWa)
10a: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYa)
10b: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYb)
10c: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYc)
10d: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYd)
10e: 3-[DODECYL(DIMETHYL)AMMONIO]PROPAN... (SBYe)
11a: IRON/SULFUR CLUSTER (SF4a)
11b: IRON/SULFUR CLUSTER (SF4b)
11c: IRON/SULFUR CLUSTER (SF4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
CSS
1
Mod. Amino Acid
S-MERCAPTOCYSTEINE
3
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
FE2
1
Ligand/Ion
FE (II) ION
5
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)
6
GOL
1
Ligand/Ion
GLYCEROL
7
NI
1
Ligand/Ion
NICKEL (II) ION
8
OCS
1
Mod. Amino Acid
CYSTEINESULFONIC ACID
9
PSW
1
Mod. Amino Acid
3-(SULFANYLSELANYL)-L-ALANINE
10
SBY
5
Ligand/Ion
3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
11
SF4
3
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , CYS A:232 , ARG A:233 , CYS A:238 , VAL A:260
BINDING SITE FOR RESIDUE SF4 A 284
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 A 285
03
AC3
SOFTWARE
GLY A:17 , CYS A:18 , CSS A:21 , GLU A:77 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , HIS B:185
BINDING SITE FOR RESIDUE SF4 A 286
04
AC4
SOFTWARE
LEU A:26 , ILE A:33 , LEU A:37 , HIS A:46 , GLU B:167
BINDING SITE FOR RESIDUE SBY A1285
05
AC5
SOFTWARE
PRO A:8 , VAL A:170 , LEU A:174
BINDING SITE FOR RESIDUE SBY A1286
06
AC6
SOFTWARE
CYS B:78 , 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:501
BINDING SITE FOR RESIDUE FCO B 500
07
AC7
SOFTWARE
OCS B:75 , CYS B:78 , PSW B:489 , CYS B:492 , FCO B:500
BINDING SITE FOR RESIDUE NI B 501
08
AC8
SOFTWARE
GLU B:56 , ILE B:441 , HIS B:495 , HOH B:2059 , HOH B:2060 , HOH B:2304
BINDING SITE FOR RESIDUE FE2 B 502
09
AC9
SOFTWARE
CYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421
BINDING SITE FOR RESIDUE CL B 504
10
BC1
SOFTWARE
ASP A:103 , HOH A:2109 , SER B:230 , LYS B:231 , LYS B:233 , LEU B:352 , HOH B:2363
BINDING SITE FOR RESIDUE GOL B1498
11
BC2
SOFTWARE
GLN B:128 , VAL B:131 , PRO B:134 , PHE B:139 , TYR B:162 , SBY B:1500
BINDING SITE FOR RESIDUE SBY B1499
12
BC3
SOFTWARE
TYR B:162 , SBY B:1499
BINDING SITE FOR RESIDUE SBY B1500
13
BC4
SOFTWARE
ASN A:111 , HOH A:2113 , PHE B:236 , ILE B:355 , LEU B:363
BINDING SITE FOR RESIDUE SBY B1501
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3ze6a_ (A:)
2a: SCOP_d3ze6b_ (B:)
View:
Select:
Label:
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 vulgaris [TaxId: 882]
(6)
1a
d3ze6a_
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
d3ze6b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 A
Chain B
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 (265 KB)
Header - Asym.Unit
Biol.Unit 1 (255 KB)
Header - Biol.Unit 1
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
3ZE6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help