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.
3MYR
Asym. Unit
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (277 KB)
Biol.Unit 2 (279 KB)
Biol.Unit 3 (279 KB)
Biol.Unit 4 (280 KB)
Biol.Unit 5 (546 KB)
Biol.Unit 6 (548 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 [NIFE] HYDROGENASE FROM ALLOCHROMATIUM VINOSUM IN ITS NI-A STATE
Authors
:
H. Ogata, P. Kellers, W. Lubitz
Date
:
11 May 10 (Deposition) - 04 Aug 10 (Release) - 06 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: E,F,G,H (1x)
Keywords
:
[Nife] Hydrogenase, Allochromatium Vinosum, Photosynthetic Purple- Sulfur Bacterium, Iron-Sulfur Cluster, Ni-A State, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ogata, P. Kellers, W. Lubitz
The Crystal Structure Of The [Nife] Hydrogenase From The Photosynthetic Bacterium Allochromatium Vinosum: Characterization Of The Oxidized Enzyme (Ni-A State).
J. Mol. Biol. V. 402 428 2010
[
close entry info
]
Hetero Components
(6, 26)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
2d: FE3-S4 CLUSTER (F3Sd)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: NI-FE OXIDIZED ACTIVE CENTER (NFVa)
5b: NI-FE OXIDIZED ACTIVE CENTER (NFVb)
5c: NI-FE OXIDIZED ACTIVE CENTER (NFVc)
5d: NI-FE OXIDIZED ACTIVE CENTER (NFVd)
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)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
F3S
4
Ligand/Ion
FE3-S4 CLUSTER
3
IMD
2
Ligand/Ion
IMIDAZOLE
4
MG
4
Ligand/Ion
MAGNESIUM ION
5
NFV
4
Ligand/Ion
NI-FE OXIDIZED ACTIVE CENTER
6
SF4
8
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(26, 26)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:15 , CYS A:16 , THR A:17 , GLY A:18 , CYS A:19 , ASP A:75 , GLY A:113 , THR A:114 , CYS A:115 , GLY A:148 , CYS A:149 , PRO A:150 , ARG B:1059
BINDING SITE FOR RESIDUE SF4 A 2001
02
AC2
SOFTWARE
HIS A:187 , CYS A:190 , ARG A:192 , ARG A:193 , CYS A:215 , LEU A:216 , CYS A:221
BINDING SITE FOR RESIDUE SF4 A 2002
03
AC3
SOFTWARE
THR A:226 , ASN A:228 , CYS A:230 , TRP A:235 , CYS A:249 , LEU A:250 , CYS A:252
BINDING SITE FOR RESIDUE F3S A 2003
04
AC4
SOFTWARE
VAL A:143 , ASN A:145 , GLY A:176 , HOH A:3657 , ARG G:139 , HOH G:5826
BINDING SITE FOR RESIDUE IMD A 3002
05
AC5
SOFTWARE
PRO A:153 , MET A:154 , ASN A:236 , ASP A:237 , HOH A:3328
BINDING SITE FOR RESIDUE CL A 2004
06
AC6
SOFTWARE
CYS B:1061 , CYS B:1064 , VAL B:1067 , HIS B:1068 , ALA B:1485 , PRO B:1486 , ARG B:1487 , LEU B:1490 , VAL B:1508 , PRO B:1509 , SER B:1510 , CYS B:1555 , CYS B:1558
BINDING SITE FOR RESIDUE NFV B 2005
07
AC7
SOFTWARE
GLU B:1042 , ALA B:1506 , HIS B:1561 , HOH B:2007 , HOH B:2008 , HOH B:2009
BINDING SITE FOR RESIDUE MG B 2006
08
AC8
SOFTWARE
PRO C:153 , MET C:154 , ASN C:236 , ASP C:237 , HOH C:3354
BINDING SITE FOR RESIDUE CL C 2004
09
AC9
SOFTWARE
GLU C:15 , CYS C:16 , THR C:17 , GLY C:18 , CYS C:19 , ASP C:75 , GLY C:113 , THR C:114 , CYS C:115 , GLY C:148 , CYS C:149 , PRO C:150 , HOH C:5613
BINDING SITE FOR RESIDUE SF4 C 2001
10
BC1
SOFTWARE
ILE C:186 , HIS C:187 , CYS C:190 , ARG C:192 , ARG C:193 , CYS C:215 , LEU C:216 , CYS C:221
BINDING SITE FOR RESIDUE SF4 C 2002
11
BC2
SOFTWARE
THR C:226 , ASN C:228 , CYS C:230 , TRP C:235 , PRO C:242 , CYS C:249 , LEU C:250 , CYS C:252 , LYS D:1211
BINDING SITE FOR RESIDUE F3S C 2003
12
BC3
SOFTWARE
CYS D:1061 , CYS D:1064 , VAL D:1067 , HIS D:1068 , ALA D:1485 , PRO D:1486 , ARG D:1487 , LEU D:1490 , VAL D:1508 , PRO D:1509 , SER D:1510 , CYS D:1555 , CYS D:1558
BINDING SITE FOR RESIDUE NFV D 2005
13
BC4
SOFTWARE
GLU D:1042 , ALA D:1506 , HIS D:1561 , HOH D:2007 , HOH D:2008 , HOH D:2009
BINDING SITE FOR RESIDUE MG D 2006
14
BC5
SOFTWARE
GLU E:15 , CYS E:16 , THR E:17 , GLY E:18 , CYS E:19 , ASP E:75 , GLY E:113 , THR E:114 , CYS E:115 , GLY E:148 , CYS E:149 , PRO E:150 , HOH E:5628 , ARG F:1059 , HIS F:1214
BINDING SITE FOR RESIDUE SF4 E 2001
15
BC6
SOFTWARE
ILE E:186 , HIS E:187 , CYS E:190 , ARG E:192 , ARG E:193 , CYS E:215 , LEU E:216 , CYS E:221
BINDING SITE FOR RESIDUE SF4 E 2002
16
BC7
SOFTWARE
THR E:226 , ASN E:228 , CYS E:230 , TRP E:235 , PRO E:242 , CYS E:249 , LEU E:250 , CYS E:252 , LYS F:1211
BINDING SITE FOR RESIDUE F3S E 2003
17
BC8
SOFTWARE
PRO E:153 , MET E:154 , ASN E:236 , ASP E:237
BINDING SITE FOR RESIDUE CL E 2004
18
BC9
SOFTWARE
CYS F:1061 , CYS F:1064 , VAL F:1067 , HIS F:1068 , ALA F:1485 , PRO F:1486 , ARG F:1487 , VAL F:1508 , PRO F:1509 , SER F:1510 , CYS F:1555 , CYS F:1558
BINDING SITE FOR RESIDUE NFV F 2005
19
CC1
SOFTWARE
GLU F:1042 , ALA F:1506 , HIS F:1561 , HOH F:2007 , HOH F:2008 , HOH F:2009
BINDING SITE FOR RESIDUE MG F 2006
20
CC2
SOFTWARE
GLU G:15 , CYS G:16 , THR G:17 , GLY G:18 , CYS G:19 , ASP G:75 , GLY G:113 , THR G:114 , CYS G:115 , GLY G:148 , CYS G:149 , PRO G:150 , HIS H:1214
BINDING SITE FOR RESIDUE SF4 G 2001
21
CC3
SOFTWARE
HIS G:187 , CYS G:190 , ARG G:192 , ARG G:193 , CYS G:215 , LEU G:216 , CYS G:221
BINDING SITE FOR RESIDUE SF4 G 2002
22
CC4
SOFTWARE
ASN G:228 , CYS G:230 , TRP G:235 , TRP G:241 , CYS G:249 , LEU G:250 , CYS G:252 , LYS H:1211
BINDING SITE FOR RESIDUE F3S G 2003
23
CC5
SOFTWARE
PRO G:153 , MET G:154 , ASN G:236 , ASP G:237 , HOH G:3053
BINDING SITE FOR RESIDUE CL G 2004
24
CC6
SOFTWARE
ARG A:139 , HOH A:4142 , MET G:135 , VAL G:143 , ASN G:145 , GLY G:176 , HOH G:4119
BINDING SITE FOR RESIDUE IMD G 3001
25
CC7
SOFTWARE
CYS H:1061 , CYS H:1064 , VAL H:1067 , HIS H:1068 , ALA H:1485 , PRO H:1486 , ARG H:1487 , LEU H:1490 , VAL H:1508 , PRO H:1509 , SER H:1510 , CYS H:1555 , CYS H:1558
BINDING SITE FOR RESIDUE NFV H 2005
26
CC8
SOFTWARE
GLU H:1042 , ALA H:1506 , HIS H:1561 , HOH H:2007 , HOH H:2008 , HOH H:2009
BINDING SITE FOR RESIDUE MG H 2006
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d3myra_ (A:)
1b: SCOP_d3myrc_ (C:)
1c: SCOP_d3myre_ (E:)
1d: SCOP_d3myrg_ (G:)
2a: SCOP_d3myrb_ (B:)
2b: SCOP_d3myrd_ (D:)
2c: SCOP_d3myrf_ (F:)
2d: SCOP_d3myrh_ (H:)
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)
Allochromatium vinosum [TaxId: 1049]
(1)
1a
d3myra_
A:
1b
d3myrc_
C:
1c
d3myre_
E:
1d
d3myrg_
G:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Allochromatium vinosum [TaxId: 1049]
(1)
2a
d3myrb_
B:
2b
d3myrd_
D:
2c
d3myrf_
F:
2d
d3myrh_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_3myrH01 (H:1039-1561)
1b: PFAM_NiFeSe_Hases_3myrH02 (H:1039-1561)
1c: PFAM_NiFeSe_Hases_3myrH03 (H:1039-1561)
1d: PFAM_NiFeSe_Hases_3myrH04 (H:1039-1561)
2a: PFAM_Oxidored_q6_3myrG01 (G:16-163)
2b: PFAM_Oxidored_q6_3myrG02 (G:16-163)
2c: PFAM_Oxidored_q6_3myrG03 (G:16-163)
2d: PFAM_Oxidored_q6_3myrG04 (G:16-163)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / D) (Chromatium vinosum)
(1)
1a
NiFeSe_Hases-3myrH01
H:1039-1561
1b
NiFeSe_Hases-3myrH02
H:1039-1561
1c
NiFeSe_Hases-3myrH03
H:1039-1561
1d
NiFeSe_Hases-3myrH04
H:1039-1561
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / D) (Chromatium vinosum)
(1)
2a
Oxidored_q6-3myrG01
G:16-163
2b
Oxidored_q6-3myrG02
G:16-163
2c
Oxidored_q6-3myrG03
G:16-163
2d
Oxidored_q6-3myrG04
G:16-163
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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 (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (277 KB)
Header - Biol.Unit 1
Biol.Unit 2 (279 KB)
Header - Biol.Unit 2
Biol.Unit 3 (279 KB)
Header - Biol.Unit 3
Biol.Unit 4 (280 KB)
Header - Biol.Unit 4
Biol.Unit 5 (546 KB)
Header - Biol.Unit 5
Biol.Unit 6 (548 KB)
Header - Biol.Unit 6
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
3MYR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help