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.
5LG8
Asym. Unit
Info
Asym.Unit (43 KB)
Biol.Unit 1 (809 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN L-TYPE FERRITIN IRON LOADED FOR 60 MINUTES
Authors
:
C. Pozzi, F. Di Pisa, S. Mangani
Date
:
06 Jul 16 (Deposition) - 22 Feb 17 (Release) - 22 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.98
Chains
:
Asym. Unit : A
Biol. Unit 1: A (24x)
Keywords
:
L-Type, Ferritin, Mineralization, Iron, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Pozzi, S. Ciambellotti, C. Bernacchioni, F. Di Pisa, S. Mangani, P. Turano
Chemistry At The Protein-Mineral Interface In L-Ferritin Assists The Assembly Of A Functional ( Mu (3)-Oxo)Tris[( Mu (2)-Peroxo)] Triiron(Iii) Cluster.
Proc. Natl. Acad. Sci. V. 114 2580 2017 U. S. A.
[
close entry info
]
Hetero Components
(5, 17)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
3a: OXYGEN MOLECULE (OXYa)
4a: PEROXIDE ION (PERa)
4b: PEROXIDE ION (PERb)
4c: PEROXIDE ION (PERc)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
8
Ligand/Ion
CADMIUM ION
2
FE
4
Ligand/Ion
FE (III) ION
3
OXY
1
Ligand/Ion
OXYGEN MOLECULE
4
PER
3
Ligand/Ion
PEROXIDE ION
5
SO4
1
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:15 , HOH A:432 , HOH A:445
binding site for residue CD A 201
02
AC2
SOFTWARE
ASP A:131
binding site for residue CD A 202
03
AC3
SOFTWARE
CYS A:130 , GLU A:134
binding site for residue CD A 203
04
AC4
SOFTWARE
HIS A:118 , CYS A:130 , GLU A:134 , HOH A:484
binding site for residue CD A 204
05
AC5
SOFTWARE
HIS A:136 , HOH A:449 , HOH A:464
binding site for residue CD A 205
06
AC6
SOFTWARE
GLU A:90 , HOH A:395 , HOH A:416 , HOH A:450
binding site for residue CD A 206
07
AC7
SOFTWARE
GLU A:49 , ASP A:178
binding site for residue CD A 207
08
AC8
SOFTWARE
GLU A:90
binding site for residue CD A 208
09
AC9
SOFTWARE
GLU A:61 , GLU A:64 , FE A:210 , FE A:211 , OXY A:213 , PER A:214 , PER A:216 , HOH A:383
binding site for residue FE A 209
10
AD1
SOFTWARE
GLU A:57 , GLU A:60 , GLU A:61 , FE A:209 , FE A:211 , OXY A:213 , PER A:215 , PER A:216
binding site for residue FE A 210
11
AD2
SOFTWARE
GLU A:60 , GLU A:64 , FE A:209 , FE A:210 , OXY A:213 , PER A:214 , PER A:215 , HOH A:382
binding site for residue FE A 211
12
AD3
SOFTWARE
GLU A:57 , PER A:215 , HOH A:457 , HOH A:496
binding site for residue FE A 212
13
AD4
SOFTWARE
GLU A:60 , GLU A:61 , GLU A:64 , FE A:209 , FE A:210 , FE A:211 , PER A:214 , PER A:215 , PER A:216
binding site for residue OXY A 213
14
AD5
SOFTWARE
GLU A:64 , FE A:209 , FE A:211 , OXY A:213 , PER A:216 , HOH A:383
binding site for residue PER A 214
15
AD6
SOFTWARE
GLU A:57 , GLU A:60 , FE A:210 , FE A:211 , FE A:212 , OXY A:213 , HOH A:388
binding site for residue PER A 215
16
AD7
SOFTWARE
GLU A:57 , GLU A:61 , FE A:209 , FE A:210 , OXY A:213 , PER A:214
binding site for residue PER A 216
17
AD8
SOFTWARE
SER A:13 , ASP A:15 , ARG A:124 , HOH A:318 , HOH A:327 , HOH A:364 , HOH A:415 , HOH A:432
binding site for residue SO4 A 217
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (43 KB)
Header - Asym.Unit
Biol.Unit 1 (809 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
5LG8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help