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.
3USE
Biol. Unit 1
Info
Asym.Unit (620 KB)
Biol.Unit 1 (310 KB)
Biol.Unit 2 (307 KB)
Biol.Unit 3 (609 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI HYDROGENASE-1 IN ITS AS-ISOLATED FORM
Authors
:
A. Volbeda, J. C. Fontecilla-Camps, C. Darnault
Date
:
23 Nov 11 (Deposition) - 28 Mar 12 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.67
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
:
Membrane-Bound Hydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, P. Amara, C. Darnault, J. M. Mouesca, A. Parkin, M. M. Roessler, F. A. Armstrong, J. C. Fontecilla-Camps
X-Ray Crystallographic And Computational Studies Of The O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli.
Proc. Natl. Acad. Sci. Usa V. 109 5305 2012
[
close entry info
]
Hetero Components
(9, 11)
Info
All Hetero Components
1a: NICKEL (III) ION (3NIa)
1b: NICKEL (III) ION (3NIb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: FE3-S4 CLUSTER (F3Sa)
3b: FE3-S4 CLUSTER (F3Sb)
4a: FE4-S3 CLUSTER (F4Sa)
4b: FE4-S3 CLUSTER (F4Sb)
5a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
5b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
7a: LITHIUM ION (LIa)
7b: LITHIUM ION (LIb)
8a: DODECYL-BETA-D-MALTOSIDE (LMTa)
8b: DODECYL-BETA-D-MALTOSIDE (LMTb)
9a: MAGNESIUM ION (MGa)
9b: MAGNESIUM ION (MGb)
10a: FE4-S3 CLUSTER (SF3a)
10b: FE4-S3 CLUSTER (SF3b)
11a: IRON/SULFUR CLUSTER (SF4a)
11b: IRON/SULFUR CLUSTER (SF4b)
12a: SULFATE ION (SO4a)
12b: SULFATE ION (SO4b)
12c: SULFATE ION (SO4c)
12d: SULFATE ION (SO4d)
12e: SULFATE ION (SO4e)
12f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3NI
1
Ligand/Ion
NICKEL (III) ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
4
F4S
1
Ligand/Ion
FE4-S3 CLUSTER
5
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
6
GOL
2
Ligand/Ion
GLYCEROL
7
LI
-1
Ligand/Ion
LITHIUM ION
8
LMT
1
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
9
MG
-1
Ligand/Ion
MAGNESIUM ION
10
SF3
1
Ligand/Ion
FE4-S3 CLUSTER
11
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
12
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(16, 16)
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: CC2 (SOFTWARE)
16: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221
BINDING SITE FOR RESIDUE SF4 S 401
02
AC2
SOFTWARE
LYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , PRO S:242 , CYS S:249 , LEU S:250 , CYS S:252
BINDING SITE FOR RESIDUE F3S S 402
03
AC3
SOFTWARE
GLU S:16 , CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , GLU S:76 , THR S:114 , CYS S:115 , CYS S:120 , GLY S:148 , CYS S:149
BINDING SITE FOR RESIDUE F4S S 403
04
AC4
SOFTWARE
GLU S:16 , CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , GLU S:76 , THR S:114 , CYS S:115 , CYS S:120 , GLY S:148 , CYS S:149
BINDING SITE FOR RESIDUE SF3 S 404
05
AC5
SOFTWARE
ILE S:7 , VAL S:9 , TRP S:11 , ILE S:72 , MET S:163 , ASP S:167 , ARG S:168
BINDING SITE FOR RESIDUE LMT S 405
06
AC6
SOFTWARE
LEU L:482 , ALA L:483 , ARG S:211
BINDING SITE FOR RESIDUE SO4 S 406
07
AC7
SOFTWARE
LYS S:218 , ARG S:266
BINDING SITE FOR RESIDUE SO4 S 407
08
AC8
SOFTWARE
TRP S:118 , CYS S:120 , GLY S:256 , HOH S:550
BINDING SITE FOR RESIDUE CL S 408
09
AC9
SOFTWARE
CYS L:79 , VAL L:82 , HIS L:83 , ALA L:507 , PRO L:508 , ARG L:509 , LEU L:512 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:579 , 3NI L:602 , HOH L:701
BINDING SITE FOR RESIDUE FCO L 601
10
BC1
SOFTWARE
CYS L:76 , CYS L:79 , CYS L:576 , CYS L:579 , FCO L:601 , HOH L:701 , HOH L:702
BINDING SITE FOR RESIDUE 3NI L 602
11
BC2
SOFTWARE
GLU L:57 , CYS L:528 , HIS L:582 , HOH L:703 , HOH L:704 , HOH L:705
BINDING SITE FOR RESIDUE MG L 603
12
BC3
SOFTWARE
ASN L:390 , GLN L:392 , HOH L:927
BINDING SITE FOR RESIDUE LI L 604
13
BC4
SOFTWARE
PHE L:331 , HIS L:421 , GLN L:446 , HOH L:1007 , HOH L:1036 , HOH L:1052 , HOH L:1071
BINDING SITE FOR RESIDUE GOL L 605
14
BC5
SOFTWARE
LEU L:135 , LEU L:179 , PHE L:182 , ARG L:183 , ASN L:184 , GLY L:185 , TRP L:187 , HOH L:1108 , LYS M:489 , HOH M:1082 , HOH M:1134
BINDING SITE FOR RESIDUE GOL L 606
15
CC2
SOFTWARE
LYS L:171 , LEU M:482 , ALA M:483 , ARG T:211
BINDING SITE FOR RESIDUE SO4 T 406
16
CC9
SOFTWARE
ASN M:375 , ARG M:394 , ARG S:125
BINDING SITE FOR RESIDUE SO4 M 604
[
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
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (L:54-79)
2: NI_HGENASE_L_2 (L:573-582)
;
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.
MBHL_ECOLI
54-79
1
L:54-79
-
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
MBHL_ECOLI
573-582
1
L:573-582
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3uses_ (S:)
1b: SCOP_d3uset_ (T:)
2a: SCOP_d3usel_ (L:)
2b: SCOP_d3usem_ (M:)
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
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Escherichia coli [TaxId: 562]
(3)
1a
d3uses_
S:
1b
d3uset_
T:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Escherichia coli [TaxId: 562]
(3)
2a
d3usel_
L:
2b
d3usem_
M:
[
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 L
Chain S
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 (620 KB)
Header - Asym.Unit
Biol.Unit 1 (310 KB)
Header - Biol.Unit 1
Biol.Unit 2 (307 KB)
Header - Biol.Unit 2
Biol.Unit 3 (609 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
3USE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
