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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2UX1
Asym. Unit
Info
Asym.Unit (326 KB)
Biol.Unit 1 (316 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
IDENTIFICATION OF TWO ZINC-BINDING SITES IN THE STREPTOCOCCUS SUIS DPR PROTEIN
Authors
:
H. Havukainen, A. Kauko, A. T. Pulliainen, S. Haataja, W. Meyer-Klauck J. Finne, A. C. Papageorgiou
Date
:
26 Mar 07 (Deposition) - 27 May 08 (Release) - 09 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Metal-Binding, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Havukainen, S. Haataja, A. Kauko, A. T. Pulliainen, A. Salminen, T. Haikarainen, J. Finne, A. C. Papageorgiou
Structural Basis Of The Zinc- And Terbium-Mediated Inhibition Of Ferroxidase Activity In Dps Ferritin- Like Proteins.
Protein Sci. V. 17 1513 2008
[
close entry info
]
Hetero Components
(4, 34)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEb)
3c: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEc)
3d: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
4m: ZINC ION (ZNm)
4n: ZINC ION (ZNn)
4o: ZINC ION (ZNo)
4p: ZINC ION (ZNp)
4q: ZINC ION (ZNq)
4r: ZINC ION (ZNr)
4s: ZINC ION (ZNs)
4t: ZINC ION (ZNt)
4u: ZINC ION (ZNu)
4v: ZINC ION (ZNv)
4w: ZINC ION (ZNw)
4x: ZINC ION (ZNx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
4
ZN
24
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(34, 34)
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)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:2097 , HOH D:2076 , HOH D:2077 , HOH D:2082 , HOH G:2083
BINDING SITE FOR RESIDUE CA D 173
02
AC2
SOFTWARE
ILE C:57 , HOH C:2077 , ARG E:53 , GLY E:54 , ASP E:137 , HOH E:2079 , HOH E:2080 , GLY L:54 , ILE L:57
BINDING SITE FOR RESIDUE EPE E 173
03
AC3
SOFTWARE
ILE H:111 , HOH H:2014
BINDING SITE FOR RESIDUE CL H 173
04
AC4
SOFTWARE
ASN G:108 , HOH G:2052 , ASN H:108 , HOH H:2013 , HOH K:2089
BINDING SITE FOR RESIDUE CA H 174
05
AC5
SOFTWARE
ARG D:53 , GLY D:54 , HOH D:2119 , GLY G:54 , HOH G:2081 , GLY I:54 , ILE I:57 , HOH I:2093 , HOH I:2094
BINDING SITE FOR RESIDUE EPE I 173
06
AC6
SOFTWARE
HOH A:2062 , HOH D:2121 , HOH I:2053 , HOH I:2054 , HOH I:2056
BINDING SITE FOR RESIDUE CA I 174
07
AC7
SOFTWARE
GLY B:54 , HOH B:2088 , ARG F:53 , GLY J:54 , HOH J:2079 , HOH J:2086 , HOH J:2087 , ASP K:137 , GLU K:138
BINDING SITE FOR RESIDUE EPE J 173
08
AC8
SOFTWARE
HOH A:2013 , HOH A:2095 , GLU G:112 , ARG H:53 , GLY H:54 , HOH H:2091 , ARG K:53 , ILE K:57 , HOH K:2088
BINDING SITE FOR RESIDUE EPE K 173
09
AC9
SOFTWARE
LEU F:166 , HOH F:2068 , HOH F:2099 , ASP K:24 , GLU K:139 , HOH K:2075 , HOH K:2076
BINDING SITE FOR RESIDUE CA K 174
10
BC1
SOFTWARE
HOH C:2079 , HOH L:2056 , HOH L:2058
BINDING SITE FOR RESIDUE CL L 173
11
BC2
SOFTWARE
ASP E:74 , GLU E:78 , HOH E:2081 , HOH E:2082 , HIS G:47
BINDING SITE FOR RESIDUE ZN E1173
12
BC3
SOFTWARE
HIS G:40 , HIS G:44
BINDING SITE FOR RESIDUE ZN G1173
13
BC4
SOFTWARE
HIS E:40 , HIS E:44 , HOH E:2083
BINDING SITE FOR RESIDUE ZN E1174
14
BC5
SOFTWARE
HIS E:47 , ASP G:74 , GLU G:78 , HOH G:2090 , HOH G:2091
BINDING SITE FOR RESIDUE ZN G1174
15
BC6
SOFTWARE
HIS F:40 , HIS F:44 , HOH F:2108
BINDING SITE FOR RESIDUE ZN F1173
16
BC7
SOFTWARE
HIS H:40 , HIS H:44 , HOH H:2096 , HOH H:2097
BINDING SITE FOR RESIDUE ZN H1173
17
BC8
SOFTWARE
ASP F:74 , GLU F:78 , HOH F:2109 , HOH F:2110 , HIS H:47
BINDING SITE FOR RESIDUE ZN F1174
18
BC9
SOFTWARE
HIS F:47 , ASP H:74 , GLU H:78 , HOH H:2098 , HOH H:2099
BINDING SITE FOR RESIDUE ZN H1174
19
CC1
SOFTWARE
HIS I:40 , HIS I:44 , HOH I:2095 , HOH I:2096
BINDING SITE FOR RESIDUE ZN I1173
20
CC2
SOFTWARE
HIS K:40 , HIS K:44 , HOH K:2096 , HOH K:2097
BINDING SITE FOR RESIDUE ZN K1173
21
CC3
SOFTWARE
ASP I:74 , GLU I:78 , HOH I:2097 , HIS K:47 , HOH K:2013
BINDING SITE FOR RESIDUE ZN I1174
22
CC4
SOFTWARE
HIS I:47 , ASP K:74 , GLU K:78 , HOH K:2098 , HOH K:2099
BINDING SITE FOR RESIDUE ZN K1174
23
CC5
SOFTWARE
HIS J:40 , HIS J:44 , HOH J:2088
BINDING SITE FOR RESIDUE ZN J1173
24
CC6
SOFTWARE
HIS J:47 , ASP L:74 , GLU L:78 , HOH L:2087 , HOH L:2088
BINDING SITE FOR RESIDUE ZN L1173
25
CC7
SOFTWARE
HIS L:40 , HIS L:44 , HOH L:2089
BINDING SITE FOR RESIDUE ZN L1174
26
CC8
SOFTWARE
ASP J:74 , GLU J:78 , HOH J:2089 , HOH J:2090 , HIS L:47
BINDING SITE FOR RESIDUE ZN J1174
27
CC9
SOFTWARE
HIS A:40 , HIS A:44 , HOH A:2105 , HOH A:2106
BINDING SITE FOR RESIDUE ZN A1173
28
DC1
SOFTWARE
HIS A:47 , ASP C:74 , GLU C:78 , HOH C:2085 , HOH C:2086
BINDING SITE FOR RESIDUE ZN C1173
29
DC2
SOFTWARE
HIS D:40 , HIS D:44 , HOH D:2130 , HOH D:2131
BINDING SITE FOR RESIDUE ZN D1173
30
DC3
SOFTWARE
HIS B:47 , ASP D:74 , GLU D:78 , HOH D:2132 , HOH D:2133
BINDING SITE FOR RESIDUE ZN D1174
31
DC4
SOFTWARE
HIS C:40 , HIS C:44 , HOH C:2087
BINDING SITE FOR RESIDUE ZN C1174
32
DC5
SOFTWARE
ASP A:74 , GLU A:78 , HOH A:2107 , HOH A:2108 , HIS C:47
BINDING SITE FOR RESIDUE ZN A1174
33
DC6
SOFTWARE
ASP B:74 , GLU B:78 , HOH B:2096 , HOH B:2097 , HIS D:47
BINDING SITE FOR RESIDUE ZN B1173
34
DC7
SOFTWARE
HIS B:40 , HIS B:44 , HOH B:2098
BINDING SITE FOR RESIDUE ZN B1174
[
close Site info
]
SAPs(SNPs)/Variants
(9, 108)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DPS_STRSU_001 (A27S, chain A/B/C/D/E/F/G/H/I/J/K/L, )
2: VAR_DPS_STRSU_002 (I42L, chain A/B/C/D/E/F/G/H/I/J/K/L, )
3: VAR_DPS_STRSU_003 (L91F, chain A/B/C/D/E/F/G/H/I/J/K/L, )
4: VAR_DPS_STRSU_004 (V103A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
5: VAR_DPS_STRSU_005 (L104P, chain A/B/C/D/E/F/G/H/I/J/K/L, )
6: VAR_DPS_STRSU_006 (T110M, chain A/B/C/D/E/F/G/H/I/J/K/L, )
7: VAR_DPS_STRSU_007 (A116V, chain A/B/C/D/E/F/G/H/I/J/K/L, )
8: VAR_DPS_STRSU_008 (S154N, chain A/B/C/D/E/F/G/H/I/J/K/L, )
9: VAR_DPS_STRSU_009 (K171G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DPS_STRSU_001
*
A
27
S
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
27
S
2
UniProt
VAR_DPS_STRSU_002
*
I
42
L
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
I
42
L
3
UniProt
VAR_DPS_STRSU_003
*
L
91
F
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
91
F
4
UniProt
VAR_DPS_STRSU_004
*
V
103
A
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
V
103
A
5
UniProt
VAR_DPS_STRSU_005
*
L
104
P
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
104
P
6
UniProt
VAR_DPS_STRSU_006
*
T
110
M
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
T
110
M
7
UniProt
VAR_DPS_STRSU_007
*
A
116
V
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
116
V
8
UniProt
VAR_DPS_STRSU_008
*
S
154
N
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
S
154
N
9
UniProt
VAR_DPS_STRSU_009
*
K
171
G
DPS_STRSU
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
171
G
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2ux1a_ (A:)
1b: SCOP_d2ux1b_ (B:)
1c: SCOP_d2ux1k_ (K:)
1d: SCOP_d2ux1l_ (L:)
1e: SCOP_d2ux1c_ (C:)
1f: SCOP_d2ux1d_ (D:)
1g: SCOP_d2ux1e_ (E:)
1h: SCOP_d2ux1f_ (F:)
1i: SCOP_d2ux1g_ (G:)
1j: SCOP_d2ux1h_ (H:)
1k: SCOP_d2ux1i_ (I:)
1l: SCOP_d2ux1j_ (J:)
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
:
Dodecameric ferritin homolog
(44)
Streptococcus suis [TaxId: 1307]
(8)
1a
d2ux1a_
A:
1b
d2ux1b_
B:
1c
d2ux1k_
K:
1d
d2ux1l_
L:
1e
d2ux1c_
C:
1f
d2ux1d_
D:
1g
d2ux1e_
E:
1h
d2ux1f_
F:
1i
d2ux1g_
G:
1j
d2ux1h_
H:
1k
d2ux1i_
I:
1l
d2ux1j_
J:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2ux1G00 (G:8-172)
1b: CATH_2ux1I00 (I:20-172)
1c: CATH_2ux1D00 (D:21-172)
1d: CATH_2ux1F00 (F:21-172)
1e: CATH_2ux1H00 (H:21-172)
1f: CATH_2ux1J00 (J:21-172)
1g: CATH_2ux1K00 (K:21-172)
1h: CATH_2ux1L00 (L:21-172)
1i: CATH_2ux1A00 (A:22-172)
1j: CATH_2ux1B00 (B:22-172)
1k: CATH_2ux1C00 (C:22-172)
1l: CATH_2ux1E00 (E:23-172)
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)
Streptococcus suis. Organism_taxid: 1307. Strain: d282.
(5)
1a
2ux1G00
G:8-172
1b
2ux1I00
I:20-172
1c
2ux1D00
D:21-172
1d
2ux1F00
F:21-172
1e
2ux1H00
H:21-172
1f
2ux1J00
J:21-172
1g
2ux1K00
K:21-172
1h
2ux1L00
L:21-172
1i
2ux1A00
A:22-172
1j
2ux1B00
B:22-172
1k
2ux1C00
C:22-172
1l
2ux1E00
E:23-172
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Ferritin_2ux1L01 (L:26-172)
1b: PFAM_Ferritin_2ux1L02 (L:26-172)
1c: PFAM_Ferritin_2ux1L03 (L:26-172)
1d: PFAM_Ferritin_2ux1L04 (L:26-172)
1e: PFAM_Ferritin_2ux1L05 (L:26-172)
1f: PFAM_Ferritin_2ux1L06 (L:26-172)
1g: PFAM_Ferritin_2ux1L07 (L:26-172)
1h: PFAM_Ferritin_2ux1L08 (L:26-172)
1i: PFAM_Ferritin_2ux1L09 (L:26-172)
1j: PFAM_Ferritin_2ux1L10 (L:26-172)
1k: PFAM_Ferritin_2ux1L11 (L:26-172)
1l: PFAM_Ferritin_2ux1L12 (L:26-172)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Streptococcus suis
(7)
1a
Ferritin-2ux1L01
L:26-172
1b
Ferritin-2ux1L02
L:26-172
1c
Ferritin-2ux1L03
L:26-172
1d
Ferritin-2ux1L04
L:26-172
1e
Ferritin-2ux1L05
L:26-172
1f
Ferritin-2ux1L06
L:26-172
1g
Ferritin-2ux1L07
L:26-172
1h
Ferritin-2ux1L08
L:26-172
1i
Ferritin-2ux1L09
L:26-172
1j
Ferritin-2ux1L10
L:26-172
1k
Ferritin-2ux1L11
L:26-172
1l
Ferritin-2ux1L12
L:26-172
[
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 (326 KB)
Header - Asym.Unit
Biol.Unit 1 (316 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
2UX1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help