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.
2Z6M
Asym. Unit
Info
Asym.Unit (352 KB)
Biol.Unit 1 (688 KB)
Biol.Unit 2 (686 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 HUMAN FERRITIN H8 AS BIOTEMPLATE FOR NOBLE METAL NANOPARTICLE SYNTHESIS
Authors
:
L. Di Costanzo, D. W. Christianson
Date
:
04 Aug 07 (Deposition) - 22 Jul 08 (Release) - 08 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.72
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (4x)
Biol. Unit 2: G,H,I,J,K,L (4x)
Keywords
:
Biotemplate, Iron, Iron Storage, Metal-Binding, Oxidoreductase, Phosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Butts, J. Swift, S. G. Kang, L. Di Costanzo, D. W. Christianson, J. G. Saven, I. J. Dmochowski
Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein
Biochemistry V. 47 12729 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
2g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MPD
7
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
ZN
5
Ligand/Ion
ZINC 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
HIS A:173 , HIS D:173
BINDING SITE FOR RESIDUE ZN A 706
02
AC2
SOFTWARE
HIS G:173 , HIS J:173 , HIS K:173 , HIS L:173
BINDING SITE FOR RESIDUE ZN G 707
03
AC3
SOFTWARE
HIS B:173 , HIS C:173 , HIS E:173 , HIS F:173
BINDING SITE FOR RESIDUE ZN B 708
04
AC4
SOFTWARE
HIS H:173
BINDING SITE FOR RESIDUE ZN H 709
05
AC5
SOFTWARE
HIS I:173
BINDING SITE FOR RESIDUE ZN I 710
06
AC6
SOFTWARE
ASP H:131 , GLU H:134 , ASP J:131 , GLU J:134 , HOH J:194 , ASP L:131 , GLU L:134
BINDING SITE FOR RESIDUE CA H 811
07
AC7
SOFTWARE
ASP A:131 , GLU A:134 , ASP C:131 , GLU C:134 , ASP E:131 , GLU E:134 , HOH E:656
BINDING SITE FOR RESIDUE CA A 812
08
AC8
SOFTWARE
ASP B:131 , GLU B:134 , ASP D:131 , GLU D:134 , ASP F:131 , GLU F:134
BINDING SITE FOR RESIDUE CA B 813
09
AC9
SOFTWARE
ASP G:131 , GLU G:134 , ASP I:131 , GLU I:134 , HOH I:718 , ASP K:131 , GLU K:134
BINDING SITE FOR RESIDUE CA G 814
10
BC1
SOFTWARE
LEU A:28 , SER A:31 , TYR A:32 , LEU F:28 , SER F:31 , TYR F:32
BINDING SITE FOR RESIDUE MPD F 533
11
BC2
SOFTWARE
SER C:31 , TYR C:32 , ARG C:63 , LEU D:28 , SER D:31 , TYR D:32 , ARG D:63
BINDING SITE FOR RESIDUE MPD C 535
12
BC3
SOFTWARE
SER G:31 , TYR G:32 , SER L:31 , TYR L:32 , ARG L:63
BINDING SITE FOR RESIDUE MPD L 537
13
BC4
SOFTWARE
SER H:31 , TYR H:32 , LEU H:35 , ARG H:63 , LEU J:28 , SER J:31
BINDING SITE FOR RESIDUE MPD H 538
14
BC5
SOFTWARE
LEU I:28 , SER I:31 , LEU K:28 , SER K:31 , TYR K:32
BINDING SITE FOR RESIDUE MPD I 539
15
BC6
SOFTWARE
LEU B:28 , SER B:31 , ARG B:63
BINDING SITE FOR RESIDUE MPD B 630
16
BC7
SOFTWARE
LEU E:28 , SER E:31 , TYR E:32 , ARG E:63
BINDING SITE FOR RESIDUE MPD E 631
[
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, 36)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (A:10-159,B:10-159,C:10-159,D:10-15...)
2: FERRITIN_1 (A:61-79,B:61-79,C:61-79,D:61-79,E:...)
3: FERRITIN_2 (A:126-146,B:126-146,C:126-146,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.
FRIH_HUMAN
11-160
12
A:10-159
B:10-159
C:10-159
D:10-159
E:10-159
F:10-159
G:10-159
H:10-159
I:10-159
J:10-159
K:10-159
L:10-159
2
FERRITIN_1
PS00540
Ferritin iron-binding regions signature 1.
FRIH_HUMAN
62-80
12
A:61-79
B:61-79
C:61-79
D:61-79
E:61-79
F:61-79
G:61-79
H:61-79
I:61-79
J:61-79
K:61-79
L:61-79
3
FERRITIN_2
PS00204
Ferritin iron-binding regions signature 2.
FRIH_HUMAN
127-147
12
A:126-146
B:126-146
C:126-146
D:126-146
E:126-146
F:126-146
G:126-146
H:126-146
I:126-146
J:126-146
K:126-146
L:126-146
[
close PROSITE info
]
Exons
(4, 48)
Info
All Exons
Exon 1.1a (A:5-37 | B:5-37 | C:5-37 | D:5-37 ...)
Exon 1.3b (A:38-86 | B:38-86 | C:38-86 | D:38...)
Exon 1.3e (A:87-128 | B:87-128 | C:87-128 | D...)
Exon 1.3l (A:129-176 | B:129-176 | C:129-176 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.3b
3: Boundary 1.3b/1.3e
4: Boundary 1.3e/1.3l
5: Boundary 1.3l/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000273550
1a
ENSE00001408170
chr11:
61735132-61734784
349
FRIH_HUMAN
1-38
38
12
A:5-37
B:5-37
C:5-37
D:5-37
E:5-37
F:5-37
G:5-37
H:5-37
I:5-37
J:5-37
K:5-37
L:5-37
33
33
33
33
33
33
33
33
33
33
33
33
1.3b
ENST00000273550
3b
ENSE00001119153
chr11:
61732987-61732841
147
FRIH_HUMAN
39-87
49
12
A:38-86
B:38-86
C:38-86
D:38-86
E:38-86
F:38-86
G:38-86
H:38-86
I:38-86
J:38-86
K:38-86
L:38-86
49
49
49
49
49
49
49
49
49
49
49
49
1.3e
ENST00000273550
3e
ENSE00001119152
chr11:
61732584-61732459
126
FRIH_HUMAN
88-129
42
12
A:87-128
B:87-128
C:87-128
D:87-128
E:87-128
F:87-128
G:87-128
H:87-128
I:87-128
J:87-128
K:87-128
L:87-128
42
42
42
42
42
42
42
42
42
42
42
42
1.3l
ENST00000273550
3l
ENSE00001430448
chr11:
61732363-61731757
607
FRIH_HUMAN
130-183
54
12
A:129-176
B:129-176
C:129-176
D:129-176
E:129-176
F:129-176
G:129-176
H:129-176
I:129-176
J:129-176
K:129-176
L:129-176
48
48
48
48
48
48
48
48
48
48
48
48
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2z6ma_ (A:)
1b: SCOP_d2z6mb_ (B:)
1c: SCOP_d2z6mc_ (C:)
1d: SCOP_d2z6md_ (D:)
1e: SCOP_d2z6me_ (E:)
1f: SCOP_d2z6mf_ (F:)
1g: SCOP_d2z6mg_ (G:)
1h: SCOP_d2z6mh_ (H:)
1i: SCOP_d2z6mi_ (I:)
1j: SCOP_d2z6mj_ (J:)
1k: SCOP_d2z6mk_ (K:)
1l: SCOP_d2z6ml_ (L:)
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)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d2z6ma_
A:
1b
d2z6mb_
B:
1c
d2z6mc_
C:
1d
d2z6md_
D:
1e
d2z6me_
E:
1f
d2z6mf_
F:
1g
d2z6mg_
G:
1h
d2z6mh_
H:
1i
d2z6mi_
I:
1j
d2z6mj_
J:
1k
d2z6mk_
K:
1l
d2z6ml_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2z6mA00 (A:5-176)
1b: CATH_2z6mB00 (B:5-176)
1c: CATH_2z6mC00 (C:5-176)
1d: CATH_2z6mD00 (D:5-176)
1e: CATH_2z6mE00 (E:5-176)
1f: CATH_2z6mF00 (F:5-176)
1g: CATH_2z6mG00 (G:5-176)
1h: CATH_2z6mH00 (H:5-176)
1i: CATH_2z6mI00 (I:5-176)
1j: CATH_2z6mJ00 (J:5-176)
1k: CATH_2z6mK00 (K:5-176)
1l: CATH_2z6mL00 (L:5-176)
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)
Human (Homo sapiens)
(16)
1a
2z6mA00
A:5-176
1b
2z6mB00
B:5-176
1c
2z6mC00
C:5-176
1d
2z6mD00
D:5-176
1e
2z6mE00
E:5-176
1f
2z6mF00
F:5-176
1g
2z6mG00
G:5-176
1h
2z6mH00
H:5-176
1i
2z6mI00
I:5-176
1j
2z6mJ00
J:5-176
1k
2z6mK00
K:5-176
1l
2z6mL00
L:5-176
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_2z6mL01 (L:17-158)
1b: PFAM_Ferritin_2z6mL02 (L:17-158)
1c: PFAM_Ferritin_2z6mL03 (L:17-158)
1d: PFAM_Ferritin_2z6mL04 (L:17-158)
1e: PFAM_Ferritin_2z6mL05 (L:17-158)
1f: PFAM_Ferritin_2z6mL06 (L:17-158)
1g: PFAM_Ferritin_2z6mL07 (L:17-158)
1h: PFAM_Ferritin_2z6mL08 (L:17-158)
1i: PFAM_Ferritin_2z6mL09 (L:17-158)
1j: PFAM_Ferritin_2z6mL10 (L:17-158)
1k: PFAM_Ferritin_2z6mL11 (L:17-158)
1l: PFAM_Ferritin_2z6mL12 (L:17-158)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Homo sapiens (Human)
(3)
1a
Ferritin-2z6mL01
L:17-158
1b
Ferritin-2z6mL02
L:17-158
1c
Ferritin-2z6mL03
L:17-158
1d
Ferritin-2z6mL04
L:17-158
1e
Ferritin-2z6mL05
L:17-158
1f
Ferritin-2z6mL06
L:17-158
1g
Ferritin-2z6mL07
L:17-158
1h
Ferritin-2z6mL08
L:17-158
1i
Ferritin-2z6mL09
L:17-158
1j
Ferritin-2z6mL10
L:17-158
1k
Ferritin-2z6mL11
L:17-158
1l
Ferritin-2z6mL12
L:17-158
[
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
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 (352 KB)
Header - Asym.Unit
Biol.Unit 1 (688 KB)
Header - Biol.Unit 1
Biol.Unit 2 (686 KB)
Header - Biol.Unit 2
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
2Z6M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help