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.
3ERZ
Asym. Unit
Info
Asym.Unit (351 KB)
Biol.Unit 1 (683 KB)
Biol.Unit 2 (683 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DIRECTING NOBLE METAL ION CHEMISTRY WITHIN A DESIGNED FERRITIN PROTEIN. MERCURY IONS ON THE THREE-FOLD CHANNEL
Authors
:
L. Di Costanzo, D. W. Christianson
Date
:
03 Oct 08 (Deposition) - 21 Oct 08 (Release) - 08 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.06
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
:
Ferritin Mutant, Nanoparticle, 3-Fold Channel, Mercury Ions, Iron, Iron Storage, Metal-Binding, Oxidoreductase, Phosphoprotein
(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
(4, 31)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: MERCURY (II) ION (HGa)
2b: MERCURY (II) ION (HGb)
2c: MERCURY (II) ION (HGc)
2d: MERCURY (II) ION (HGd)
2e: MERCURY (II) ION (HGe)
2f: MERCURY (II) ION (HGf)
2g: MERCURY (II) ION (HGg)
2h: MERCURY (II) ION (HGh)
2i: MERCURY (II) ION (HGi)
2j: MERCURY (II) ION (HGj)
2k: MERCURY (II) ION (HGk)
2l: MERCURY (II) ION (HGl)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
3i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
3j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
3k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
HG
12
Ligand/Ion
MERCURY (II) ION
3
MPD
11
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
ZN
5
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:28 , SER A:31 , TYR A:32 , LEU F:28 , SER F:31 , TYR F:32
BINDING SITE FOR RESIDUE MPD A 533
02
AC2
SOFTWARE
ASP A:126 , PRO A:127 , CYS A:130 , HOH A:823
BINDING SITE FOR RESIDUE HG A 524
03
AC3
SOFTWARE
GLU A:134 , GLU C:134 , GLU E:134
BINDING SITE FOR RESIDUE CA A 812
04
AC4
SOFTWARE
HIS A:173 , HIS D:173
BINDING SITE FOR RESIDUE ZN A 706
05
AC5
SOFTWARE
HIS B:60 , ARG B:63 , CYS B:64
BINDING SITE FOR RESIDUE MPD B 540
06
AC6
SOFTWARE
LEU B:28 , SER B:31 , ARG B:63
BINDING SITE FOR RESIDUE MPD B 630
07
AC7
SOFTWARE
ALA B:121 , ASP B:126 , CYS B:130
BINDING SITE FOR RESIDUE HG B 526
08
AC8
SOFTWARE
HIS B:173 , HIS C:173 , HIS E:173 , HIS F:173
BINDING SITE FOR RESIDUE ZN B 708
09
AC9
SOFTWARE
SER C:31 , TYR C:32 , ARG C:63 , TYR D:32 , ARG D:63
BINDING SITE FOR RESIDUE MPD C 535
10
BC1
SOFTWARE
HOH A:832 , CYS C:130
BINDING SITE FOR RESIDUE HG C 525
11
BC2
SOFTWARE
THR D:122 , CYS D:130
BINDING SITE FOR RESIDUE HG D 527
12
BC3
SOFTWARE
LEU E:28 , SER E:31 , TYR E:32 , ARG E:63
BINDING SITE FOR RESIDUE MPD E 631
13
BC4
SOFTWARE
CYS E:130
BINDING SITE FOR RESIDUE HG E 523
14
BC5
SOFTWARE
GLU F:61 , CYS F:140 , CYS F:143 , HOH F:552
BINDING SITE FOR RESIDUE MPD F 543
15
BC6
SOFTWARE
THR F:122 , ASP F:126 , PRO F:127 , CYS F:130 , HOH F:565
BINDING SITE FOR RESIDUE HG F 528
16
BC7
SOFTWARE
SER G:31 , SER L:31 , TYR L:32 , ARG L:63
BINDING SITE FOR RESIDUE MPD G 537
17
BC8
SOFTWARE
THR G:122 , CYS G:130 , HOH G:823
BINDING SITE FOR RESIDUE HG G 529
18
BC9
SOFTWARE
ASP G:131 , GLU G:134 , ASP I:131 , GLU I:134 , ASP K:131 , GLU K:134
BINDING SITE FOR RESIDUE CA G 813
19
CC1
SOFTWARE
HIS G:173 , HIS J:173 , HIS K:173 , HIS L:173
BINDING SITE FOR RESIDUE ZN G 707
20
CC2
SOFTWARE
SER H:31 , TYR H:32 , ARG H:63 , LEU J:28 , SER J:31
BINDING SITE FOR RESIDUE MPD H 538
21
CC3
SOFTWARE
ARG H:63 , CYS H:64 , HOH H:711
BINDING SITE FOR RESIDUE MPD H 542
22
CC4
SOFTWARE
CYS H:130
BINDING SITE FOR RESIDUE HG H 533
23
CC5
SOFTWARE
HIS H:173
BINDING SITE FOR RESIDUE ZN H 709
24
CC6
SOFTWARE
SER I:31 , TYR I:32 , ARG I:63 , LEU K:28 , SER K:31 , TYR K:32
BINDING SITE FOR RESIDUE MPD I 539
25
CC7
SOFTWARE
HOH G:820 , PRO I:127 , CYS I:130
BINDING SITE FOR RESIDUE HG I 531
26
CC8
SOFTWARE
HIS I:173
BINDING SITE FOR RESIDUE ZN I 710
27
CC9
SOFTWARE
THR J:122 , CYS J:130
BINDING SITE FOR RESIDUE HG J 532
28
DC1
SOFTWARE
ASP H:131 , GLU H:134 , ASP J:131 , GLU J:134 , ASP L:131 , GLU L:134 , HOH L:549
BINDING SITE FOR RESIDUE CA J 811
29
DC2
SOFTWARE
HIS K:60 , GLU K:61 , ARG K:63 , CYS K:64
BINDING SITE FOR RESIDUE MPD K 541
30
DC3
SOFTWARE
THR K:122 , CYS K:130
BINDING SITE FOR RESIDUE HG K 530
31
DC4
SOFTWARE
PRO L:127 , CYS L:130
BINDING SITE FOR RESIDUE HG L 534
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3erzA00 (A:5-176)
1b: CATH_3erzB00 (B:5-176)
1c: CATH_3erzC00 (C:5-176)
1d: CATH_3erzD00 (D:5-176)
1e: CATH_3erzE00 (E:5-176)
1f: CATH_3erzF00 (F:5-176)
1g: CATH_3erzG00 (G:5-176)
1h: CATH_3erzH00 (H:5-176)
1i: CATH_3erzI00 (I:5-176)
1j: CATH_3erzJ00 (J:5-176)
1k: CATH_3erzK00 (K:5-176)
1l: CATH_3erzL00 (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
3erzA00
A:5-176
1b
3erzB00
B:5-176
1c
3erzC00
C:5-176
1d
3erzD00
D:5-176
1e
3erzE00
E:5-176
1f
3erzF00
F:5-176
1g
3erzG00
G:5-176
1h
3erzH00
H:5-176
1i
3erzI00
I:5-176
1j
3erzJ00
J:5-176
1k
3erzK00
K:5-176
1l
3erzL00
L:5-176
[
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
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 (351 KB)
Header - Asym.Unit
Biol.Unit 1 (683 KB)
Header - Biol.Unit 1
Biol.Unit 2 (683 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
3ERZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help