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.
1Q0M
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (132 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 NI-CONTAINING SUPEROXIDE DISMUTASE WITH NI-LIGATION CORRESPONDING TO THE STATE AFTER FULL X-RAY-INDUCED REDUCTION
Authors
:
J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Date
:
16 Jul 03 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.68
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Homohexamer Of Four-Helix Bundles, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Crystal Structure Of Nickel-Containing Superoxide Dismutase Reveals Another Type Of Active Site
Proc. Natl. Acad. Sci. Usa V. 101 8569 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
NI
6
Ligand/Ion
NICKEL (II) ION
3
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:1 , CYS A:2 , ASP A:3 , CYS A:6
BINDING SITE FOR RESIDUE NI A 118
02
AC2
SOFTWARE
HIS B:1 , CYS B:2 , ASP B:3 , CYS B:6
BINDING SITE FOR RESIDUE NI B 118
03
AC3
SOFTWARE
HIS C:1 , CYS C:2 , ASP C:3 , CYS C:6
BINDING SITE FOR RESIDUE NI C 118
04
AC4
SOFTWARE
HIS D:1 , CYS D:2 , ASP D:3 , CYS D:6
BINDING SITE FOR RESIDUE NI D 118
05
AC5
SOFTWARE
HIS E:1 , CYS E:2 , ASP E:3 , CYS E:6
BINDING SITE FOR RESIDUE NI E 118
06
AC6
SOFTWARE
HIS F:1 , CYS F:2 , ASP F:3 , CYS F:6
BINDING SITE FOR RESIDUE NI F 118
07
AC7
SOFTWARE
PRO A:5 , GLY A:7 , TYR A:9 , LYS A:64 , HOH A:9143
BINDING SITE FOR RESIDUE SO4 A 9001
08
AC8
SOFTWARE
PRO B:5 , GLY B:7 , TYR B:9 , ASP B:61 , LYS B:64 , HOH B:9046 , HOH B:9060 , HOH B:9119 , HOH B:9151
BINDING SITE FOR RESIDUE SO4 B 9002
09
AC9
SOFTWARE
PRO C:5 , GLY C:7 , TYR C:9 , ASP C:61 , LYS C:64 , HOH C:9083 , HOH C:9128 , HOH C:9137
BINDING SITE FOR RESIDUE SO4 C 9003
10
BC1
SOFTWARE
PRO D:5 , GLY D:7 , TYR D:9 , ASP D:61 , LYS D:64 , HOH D:9063
BINDING SITE FOR RESIDUE SO4 D 9004
11
BC2
SOFTWARE
PRO E:5 , GLY E:7 , TYR E:9 , ASP E:61 , LYS E:64 , HOH E:9079 , HOH E:9113
BINDING SITE FOR RESIDUE SO4 E 9005
12
BC3
SOFTWARE
PRO F:5 , GLY F:7 , TYR F:9 , LYS F:64 , HOH F:9076 , HOH F:9108
BINDING SITE FOR RESIDUE SO4 F 9006
13
BC4
SOFTWARE
GLN A:46 , GLN B:46 , GLN D:46 , HOH D:9071 , HOH D:9077
BINDING SITE FOR RESIDUE SO4 D 9007
14
BC5
SOFTWARE
GLN C:46 , HOH C:9068 , GLN E:46 , GLN F:46
BINDING SITE FOR RESIDUE SO4 C 9008
15
BC6
SOFTWARE
GLU C:69 , PRO D:65 , PHE D:68 , ASN E:79 , HOH E:9059 , HOH E:9074
BINDING SITE FOR RESIDUE ACY C 7001
16
BC7
SOFTWARE
THR B:76 , ASN B:79 , HOH B:9043 , PRO C:65 , HIS C:75 , GLU D:69
BINDING SITE FOR RESIDUE ACY D 7002
17
BC8
SOFTWARE
PRO B:65 , PHE B:68 , ASN C:79 , LYS C:83 , HOH C:9025 , HOH C:9066 , GLU F:69
BINDING SITE FOR RESIDUE ACY F 7003
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1q0ma_ (A:)
1b: SCOP_d1q0mb_ (B:)
1c: SCOP_d1q0mc_ (C:)
1d: SCOP_d1q0md_ (D:)
1e: SCOP_d1q0me_ (E:)
1f: SCOP_d1q0mf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Family
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Protein domain
:
Nickel-containing superoxide dismutase, NiSOD
(8)
Streptomyces seoulensis [TaxId: 73044]
(5)
1a
d1q0ma_
A:
1b
d1q0mb_
B:
1c
d1q0mc_
C:
1d
d1q0md_
D:
1e
d1q0me_
E:
1f
d1q0mf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1q0mA00 (A:1-117)
1b: CATH_1q0mB00 (B:1-117)
1c: CATH_1q0mC00 (C:1-117)
1d: CATH_1q0mD00 (D:1-117)
1e: CATH_1q0mE00 (E:1-117)
1f: CATH_1q0mF00 (F:1-117)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
Nickel-containing superoxide dismutase, NiSOD
(11)
Streptomyces seoulensis. Organism_taxid: 73044
(5)
1a
1q0mA00
A:1-117
1b
1q0mB00
B:1-117
1c
1q0mC00
C:1-117
1d
1q0mD00
D:1-117
1e
1q0mE00
E:1-117
1f
1q0mF00
F:1-117
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Sod_Ni_1q0mF01 (F:1-115)
1b: PFAM_Sod_Ni_1q0mF02 (F:1-115)
1c: PFAM_Sod_Ni_1q0mF03 (F:1-115)
1d: PFAM_Sod_Ni_1q0mF04 (F:1-115)
1e: PFAM_Sod_Ni_1q0mF05 (F:1-115)
1f: PFAM_Sod_Ni_1q0mF06 (F:1-115)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sod_Ni]
(8)
Family
:
Sod_Ni
(8)
Streptomyces seoulensis
(5)
1a
Sod_Ni-1q0mF01
F:1-115
1b
Sod_Ni-1q0mF02
F:1-115
1c
Sod_Ni-1q0mF03
F:1-115
1d
Sod_Ni-1q0mF04
F:1-115
1e
Sod_Ni-1q0mF05
F:1-115
1f
Sod_Ni-1q0mF06
F:1-115
[
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
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 (136 KB)
Header - Asym.Unit
Biol.Unit 1 (132 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
1Q0M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
