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.
4DAS
Asym. Unit
Info
Asym.Unit (719 KB)
Biol.Unit 1 (711 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 BULLFROG M FERRITIN
Authors
:
I. Bertini, D. Lalli, S. Mangani, C. Pozzi, C. Rosa, P. Turano
Date
:
13 Jan 12 (Deposition) - 16 Jan 13 (Release) - 24 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.56
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X (1x)
Keywords
:
Iron Storage Protein, 24-Subunit Maxiferritin, Four-Helix Bundle Subunit, Oxidoreductase, Ferroxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bertini, D. Lalli, S. Mangani, C. Pozzi, C. Rosa, E. C. Theil, P. Turano
Structural Insights Into The Ferroxidase Site Of Ferritins From Higher Eukaryotes.
J. Am. Chem. Soc. V. 134 6169 2012
[
close entry info
]
Hetero Components
(2, 34)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
2a: TRIETHYLENE GLYCOL (PGEa)
2b: TRIETHYLENE GLYCOL (PGEb)
2c: TRIETHYLENE GLYCOL (PGEc)
2d: TRIETHYLENE GLYCOL (PGEd)
2e: TRIETHYLENE GLYCOL (PGEe)
2f: TRIETHYLENE GLYCOL (PGEf)
2g: TRIETHYLENE GLYCOL (PGEg)
2h: TRIETHYLENE GLYCOL (PGEh)
2i: TRIETHYLENE GLYCOL (PGEi)
2j: TRIETHYLENE GLYCOL (PGEj)
2k: TRIETHYLENE GLYCOL (PGEk)
2l: TRIETHYLENE GLYCOL (PGEl)
2m: TRIETHYLENE GLYCOL (PGEm)
2n: TRIETHYLENE GLYCOL (PGEn)
2o: TRIETHYLENE GLYCOL (PGEo)
2p: TRIETHYLENE GLYCOL (PGEp)
2q: TRIETHYLENE GLYCOL (PGEq)
2r: TRIETHYLENE GLYCOL (PGEr)
2s: TRIETHYLENE GLYCOL (PGEs)
2t: TRIETHYLENE GLYCOL (PGEt)
2u: TRIETHYLENE GLYCOL (PGEu)
2v: TRIETHYLENE GLYCOL (PGEv)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
2
PGE
22
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(32, 32)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA B:16 , ARG B:19 , MET B:20 , ALA B:110
BINDING SITE FOR RESIDUE PGE B 201
02
AC2
SOFTWARE
SER C:28 , SER C:32 , HOH C:323 , SER O:28 , SER O:32
BINDING SITE FOR RESIDUE PGE C 201
03
AC3
SOFTWARE
ALA C:16 , ARG C:19 , ALA C:110 , ASP C:113
BINDING SITE FOR RESIDUE PGE C 202
04
AC4
SOFTWARE
ARG D:19 , MET D:20 , ASP D:113
BINDING SITE FOR RESIDUE PGE D 201
05
AC5
SOFTWARE
ALA D:44 , HIS D:46 , TYR D:165 , ASP D:168 , LYS D:169 , ASN X:151
BINDING SITE FOR RESIDUE EDO D 202
06
AC6
SOFTWARE
SER E:32 , SER I:32
BINDING SITE FOR RESIDUE PGE E 201
07
AC7
SOFTWARE
ALA F:16 , ARG F:19 , ALA F:110
BINDING SITE FOR RESIDUE PGE F 201
08
AC8
SOFTWARE
SER A:28 , SER A:32 , SER G:28 , ARG G:60 , GLU G:64
BINDING SITE FOR RESIDUE PGE G 201
09
AC9
SOFTWARE
ARG G:19 , ALA G:110 , LEU G:114
BINDING SITE FOR RESIDUE PGE G 202
10
BC1
SOFTWARE
SER D:28 , SER D:32 , MET D:67 , SER H:28 , SER H:32 , HOH H:307
BINDING SITE FOR RESIDUE PGE H 201
11
BC2
SOFTWARE
ALA H:16 , ARG H:19
BINDING SITE FOR RESIDUE PGE H 202
12
BC3
SOFTWARE
ARG I:19 , ALA I:110
BINDING SITE FOR RESIDUE PGE I 201
13
BC4
SOFTWARE
ARG J:19
BINDING SITE FOR RESIDUE EDO J 201
14
BC5
SOFTWARE
ARG L:19 , MET L:20 , ALA L:110
BINDING SITE FOR RESIDUE EDO L 201
15
BC6
SOFTWARE
ARG M:19
BINDING SITE FOR RESIDUE EDO M 201
16
BC7
SOFTWARE
ALA N:110 , HOH N:343
BINDING SITE FOR RESIDUE EDO N 201
17
BC8
SOFTWARE
ASP N:12 , ALA N:15 , ALA N:16 , ARG N:19 , HOH N:343 , ASP W:88 , GLU W:89
BINDING SITE FOR RESIDUE EDO N 202
18
BC9
SOFTWARE
LYS C:68 , LYS C:72 , ASP O:39 , HIS O:46 , LYS R:143
BINDING SITE FOR RESIDUE EDO O 201
19
CC1
SOFTWARE
ARG P:19 , MET P:20
BINDING SITE FOR RESIDUE PGE P 201
20
CC2
SOFTWARE
ARG P:87 , ASP P:88 , GLU P:89
BINDING SITE FOR RESIDUE EDO P 202
21
CC3
SOFTWARE
SER Q:32 , SER U:28 , SER U:32
BINDING SITE FOR RESIDUE PGE Q 201
22
CC4
SOFTWARE
ARG Q:19 , ALA Q:110 , ASP Q:113
BINDING SITE FOR RESIDUE PGE Q 202
23
CC5
SOFTWARE
SER N:28 , SER N:32 , SER R:28 , SER R:32
BINDING SITE FOR RESIDUE PGE R 201
24
CC6
SOFTWARE
SER K:11 , ASP K:12 , ALA K:15 , HOH K:262 , HOH K:285 , ASN N:71 , ARG N:76 , VAL N:77 , ALA R:36 , PHE R:37 , ARG R:40 , ASP R:88 , HOH R:348
BINDING SITE FOR RESIDUE PGE R 202
25
CC7
SOFTWARE
ARG R:19 , MET R:20 , ALA R:110
BINDING SITE FOR RESIDUE PGE R 203
26
CC8
SOFTWARE
ALA S:16 , ARG S:19 , ALA S:110
BINDING SITE FOR RESIDUE PGE S 201
27
CC9
SOFTWARE
ALA U:16 , ARG U:19 , ALA U:110
BINDING SITE FOR RESIDUE PGE U 201
28
DC1
SOFTWARE
ASN N:151 , ALA U:44 , LEU U:45 , HIS U:46 , TYR U:165 , ASP U:168 , LYS U:169
BINDING SITE FOR RESIDUE EDO U 202
29
DC2
SOFTWARE
ASN K:108 , LEU K:112 , GLN U:7 , ASN U:8 , ARG U:73 , ASP U:123 , HIS U:125
BINDING SITE FOR RESIDUE EDO U 203
30
DC3
SOFTWARE
ALA X:16 , ARG X:19 , MET X:20 , ALA X:110 , ASP X:113
BINDING SITE FOR RESIDUE PGE X 201
31
DC4
SOFTWARE
SER K:28 , SER K:32 , SER W:32
BINDING SITE FOR RESIDUE PGE W 201
32
DC5
SOFTWARE
ARG W:19 , ALA W:110
BINDING SITE FOR RESIDUE PGE W 202
[
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
(3, 72)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (A:7-156,B:7-156,C:7-156,D:7-156,E:...)
2: FERRITIN_1 (A:58-76,B:58-76,C:58-76,D:58-76,E:...)
3: FERRITIN_2 (A:123-143,B:123-143,C:123-143,D:12...)
;
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.
FRI2_LITCT
7-156
24
A:7-156
B:7-156
C:7-156
D:7-156
E:7-156
F:7-156
G:7-156
H:7-156
I:7-156
J:7-156
K:7-156
L:7-156
M:7-156
N:7-156
O:7-156
P:7-156
Q:7-156
R:7-156
S:7-156
T:7-156
U:7-156
V:7-156
W:7-156
X:7-156
2
FERRITIN_1
PS00540
Ferritin iron-binding regions signature 1.
FRI2_LITCT
58-76
24
A:58-76
B:58-76
C:58-76
D:58-76
E:58-76
F:58-76
G:58-76
H:58-76
I:58-76
J:58-76
K:58-76
L:58-76
M:58-76
N:58-76
O:58-76
P:58-76
Q:58-76
R:58-76
S:58-76
T:58-76
U:58-76
V:58-76
W:58-76
X:58-76
3
FERRITIN_2
PS00204
Ferritin iron-binding regions signature 2.
FRI2_LITCT
123-143
24
A:123-143
B:123-143
C:123-143
D:123-143
E:123-143
F:123-143
G:123-143
H:123-143
I:123-143
J:123-143
K:123-143
L:123-143
M:123-143
N:123-143
O:123-143
P:123-143
Q:123-143
R:123-143
S:123-143
T:123-143
U:123-143
V:123-143
W:123-143
X:123-143
[
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, 24)
Info
All SCOP Domains
1a: SCOP_d4dasa_ (A:)
1b: SCOP_d4dasc_ (C:)
1c: SCOP_d4dasd_ (D:)
1d: SCOP_d4dase_ (E:)
1e: SCOP_d4dasf_ (F:)
1f: SCOP_d4dasg_ (G:)
1g: SCOP_d4dash_ (H:)
1h: SCOP_d4dasi_ (I:)
1i: SCOP_d4dasj_ (J:)
1j: SCOP_d4dask_ (K:)
1k: SCOP_d4dasl_ (L:)
1l: SCOP_d4dasm_ (M:)
1m: SCOP_d4dasn_ (N:)
1n: SCOP_d4daso_ (O:)
1o: SCOP_d4dasp_ (P:)
1p: SCOP_d4dasq_ (Q:)
1q: SCOP_d4dasr_ (R:)
1r: SCOP_d4dass_ (S:)
1s: SCOP_d4dast_ (T:)
1t: SCOP_d4dasu_ (U:)
1u: SCOP_d4dasv_ (V:)
1v: SCOP_d4dasw_ (W:)
1w: SCOP_d4dasx_ (X:)
1x: SCOP_d4dasb_ (B:)
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
:
automated matches
(70)
Bullfrog (Rana catesbeiana) [TaxId: 8400]
(12)
1a
d4dasa_
A:
1b
d4dasc_
C:
1c
d4dasd_
D:
1d
d4dase_
E:
1e
d4dasf_
F:
1f
d4dasg_
G:
1g
d4dash_
H:
1h
d4dasi_
I:
1i
d4dasj_
J:
1j
d4dask_
K:
1k
d4dasl_
L:
1l
d4dasm_
M:
1m
d4dasn_
N:
1n
d4daso_
O:
1o
d4dasp_
P:
1p
d4dasq_
Q:
1q
d4dasr_
R:
1r
d4dass_
S:
1s
d4dast_
T:
1t
d4dasu_
U:
1u
d4dasv_
V:
1v
d4dasw_
W:
1w
d4dasx_
X:
1x
d4dasb_
B:
[
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
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
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 (719 KB)
Header - Asym.Unit
Biol.Unit 1 (711 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
4DAS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help