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2Z6M
Biol. Unit 2
Info
Asym.Unit (352 KB)
Biol.Unit 1 (688 KB)
Biol.Unit 2 (686 KB)
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(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
)
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Hetero Components
(1, 12)
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
-1
Ligand/Ion
CALCIUM ION
2
MPD
12
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(8, 8)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HIS G:173 , HIS J:173 , HIS K:173 , HIS L:173
BINDING SITE FOR RESIDUE ZN G 707
2
AC4
SOFTWARE
HIS H:173
BINDING SITE FOR RESIDUE ZN H 709
3
AC5
SOFTWARE
HIS I:173
BINDING SITE FOR RESIDUE ZN I 710
4
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
5
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
6
BC3
SOFTWARE
SER G:31 , TYR G:32 , SER L:31 , TYR L:32 , ARG L:63
BINDING SITE FOR RESIDUE MPD L 537
7
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
8
BC5
SOFTWARE
LEU I:28 , SER I:31 , LEU K:28 , SER K:31 , TYR K:32
BINDING SITE FOR RESIDUE MPD I 539
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 72)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (G:10-159,H:10-159,I:10-159,J:10-15...)
2: FERRITIN_1 (G:61-79,H:61-79,I:61-79,J:61-79,K:...)
3: FERRITIN_2 (G:126-146,H:126-146,I:126-146,J:12...)
;
View:
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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
24
-
-
-
-
-
-
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
24
-
-
-
-
-
-
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
24
-
-
-
-
-
-
G:126-146
H:126-146
I:126-146
J:126-146
K:126-146
L:126-146
[
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Exons
(0, 0)
Info
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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, 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:)
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Protein Domains
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)
(
)
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:
[
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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)
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)
(
)
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
[
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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)
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Clans
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(
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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
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