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.
2ZG8
Biol. Unit 1
Info
Asym.Unit (44 KB)
Biol.Unit 1 (824 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 PD(ALLYL)/APO-H49AFR
Authors
:
S. Abe, J. Niemeyer, M. Abe, T. Ueno, T. Hikage, G. Erker, Y. Watanabe
Date
:
18 Jan 08 (Deposition) - 26 Aug 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : X
Biol. Unit 1: X (24x)
Keywords
:
Iron Storage Protein, Light Chain Apoferritin, Artificial Metalloprotein, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Abe, J. Niemeyer, M. Abe, Y. Takezawa, T. Ueno, T. Hikage, G. Erker, Y. Watanabe
Control Of The Coordination Structure Of Organometallic Palladium Complexes In An Apo-Ferritin Cage.
J. Am. Chem. Soc. V. 130 10512 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 336)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
3a: PALLADIUM ION (PDa)
4a: PALLADIUM(II) ALLYL COMPLEX (PLLa)
4b: PALLADIUM(II) ALLYL COMPLEX (PLLb)
4c: PALLADIUM(II) ALLYL COMPLEX (PLLc)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
-1
Ligand/Ion
CADMIUM ION
2
EDO
168
Ligand/Ion
1,2-ETHANEDIOL
3
PD
-1
Ligand/Ion
PALLADIUM ION
4
PLL
72
Ligand/Ion
PALLADIUM(II) ALLYL COMPLEX
5
SO4
96
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: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS X:126 , HOH X:302
BINDING SITE FOR RESIDUE PD X 175
02
AC2
SOFTWARE
ASP X:80 , HOH X:200
BINDING SITE FOR RESIDUE CD X 176
03
AC3
SOFTWARE
GLN X:6 , ASN X:7 , HOH X:238 , HOH X:250 , HOH X:268
BINDING SITE FOR RESIDUE SO4 X 177
04
AC4
SOFTWARE
ARG X:25 , GLN X:82 , LYS X:83 , SER X:85 , HOH X:243 , HOH X:319
BINDING SITE FOR RESIDUE SO4 X 178
05
AC5
SOFTWARE
GLN X:86 , ASP X:87 , GLU X:88 , HOH X:292 , HOH X:341 , HOH X:392
BINDING SITE FOR RESIDUE SO4 X 179
06
AC6
SOFTWARE
LYS X:143 , ASP X:146 , HIS X:147 , HOH X:209 , HOH X:230 , HOH X:345 , HOH X:356
BINDING SITE FOR RESIDUE SO4 X 180
07
AC7
SOFTWARE
PHE X:35 , ASP X:38 , GLU X:45 , CYS X:48 , LYS X:67
BINDING SITE FOR RESIDUE PLL X 181
08
AC8
SOFTWARE
HIS X:114 , PRO X:123 , CYS X:126 , GLU X:130 , HOH X:302
BINDING SITE FOR RESIDUE PLL X 182
09
AC9
SOFTWARE
GLU X:45 , CYS X:48 , ALA X:49 , ARG X:52
BINDING SITE FOR RESIDUE PLL X 183
10
BC1
SOFTWARE
TYR X:36 , GLY X:90 , THR X:91 , ARG X:153 , GLU X:163 , HOH X:357 , HOH X:360
BINDING SITE FOR RESIDUE EDO X 184
11
BC2
SOFTWARE
ALA X:14 , ARG X:18 , HOH X:303 , HOH X:367
BINDING SITE FOR RESIDUE EDO X 185
12
BC3
SOFTWARE
GLU X:88 , GLY X:90 , ASP X:94
BINDING SITE FOR RESIDUE EDO X 186
13
BC4
SOFTWARE
LEU X:22 , SER X:105 , HOH X:239 , HOH X:322 , HOH X:361
BINDING SITE FOR RESIDUE EDO X 187
14
BC5
SOFTWARE
ARG X:5 , THR X:10 , GLU X:13 , HOH X:220 , HOH X:248
BINDING SITE FOR RESIDUE EDO X 188
15
BC6
SOFTWARE
SER X:27 , HOH X:310
BINDING SITE FOR RESIDUE EDO X 189
16
BC7
SOFTWARE
ARG X:168 , THR X:170 , LYS X:172 , HOH X:349 , HOH X:375
BINDING SITE FOR RESIDUE EDO X 190
[
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
(3, 72)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (X:6-155)
2: FERRITIN_1 (X:57-75)
3: FERRITIN_2 (X:122-142)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
FRIL_HORSE
7-156
24
X:6-155
2
FERRITIN_1
PS00540
Ferritin iron-binding regions signature 1.
FRIL_HORSE
58-76
24
X:57-75
3
FERRITIN_2
PS00204
Ferritin iron-binding regions signature 2.
FRIL_HORSE
123-143
24
X:122-142
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2zg8x_ (X:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
(Apo)ferritin
(68)
Horse (Equus caballus), L chain [TaxId: 9796]
(46)
1a
d2zg8x_
X:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2zg8X00 (X:1-173)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Horse (Equus caballus)
(31)
1a
2zg8X00
X:1-173
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Ferritin_2zg8X01 (X:13-154)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Equus caballus (Horse)
(23)
1a
Ferritin-2zg8X01
X:13-154
[
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 X
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
Asymmetric Unit 5
Asymmetric Unit 6
Asymmetric Unit 7
Asymmetric Unit 8
Asymmetric Unit 9
Asymmetric Unit 10
Asymmetric Unit 11
Asymmetric Unit 12
Asymmetric Unit 13
Asymmetric Unit 14
Asymmetric Unit 15
Asymmetric Unit 16
Asymmetric Unit 17
Asymmetric Unit 18
Asymmetric Unit 19
Asymmetric Unit 20
Asymmetric Unit 21
Asymmetric Unit 22
Asymmetric Unit 23
Asymmetric Unit 24
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 (44 KB)
Header - Asym.Unit
Biol.Unit 1 (824 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
2ZG8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help