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.
2R8Z
Biol. Unit 3
Info
Asym.Unit (493 KB)
Biol.Unit 1 (239 KB)
Biol.Unit 2 (252 KB)
Biol.Unit 3 (131 KB)
Biol.Unit 4 (124 KB)
Biol.Unit 5 (130 KB)
Biol.Unit 6 (123 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 YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH A PHOSPHATE AND A CALCIUM ION
Authors
:
O. V. Tsodikov, P. Aggarwal, J. R. Rubin, J. A. Stuckey, R. W. Woodard, T.
Date
:
11 Sep 07 (Deposition) - 23 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: I,J,K,L,M,N,O,P (1x)
Biol. Unit 2: A,B,C,D,E,F,G,H (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: I,J,K,L (1x)
Biol. Unit 5: E,F,G,H (1x)
Biol. Unit 6: M,N,O,P (1x)
Keywords
:
Yrbi, Phosphatase, Divalent Metal, Phosphate, Kdo8-P, Had Superfamily, Hydrolase, Lipopolysaccharide Biosynthesis, Magnesium
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Biswas, L. Yi, P. Aggarwal, J. Wu, J. R. Rubin, J. A. Stuckey, R. W. Woodard, O. V. Tsodikov
The Tail Of Kdsc: Conformational Changes Control The Activity Of A Haloacid Dehalogenase Superfamily Phosphatase
J. Biol. Chem. V. 284 30594 2009
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
2k: PHOSPHATE ION (PO4k)
2l: PHOSPHATE ION (PO4l)
2m: PHOSPHATE ION (PO4m)
2n: PHOSPHATE ION (PO4n)
2o: PHOSPHATE ION (PO4o)
2p: PHOSPHATE ION (PO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
PO4
4
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: BC8 (SOFTWARE)
6: BC9 (SOFTWARE)
7: CC1 (SOFTWARE)
8: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:32 , ASP A:34 , ASP A:125 , PO4 A:202 , HOH A:203 , HOH A:204
BINDING SITE FOR RESIDUE CA A 201
2
AC2
SOFTWARE
HOH A:302 , ASP B:32 , ASP B:34 , ASP B:125 , PO4 B:203 , HOH B:205
BINDING SITE FOR RESIDUE CA B 202
3
AC3
SOFTWARE
ASP C:32 , ASP C:34 , ASP C:125 , PO4 C:204 , HOH C:205 , HOH C:206
BINDING SITE FOR RESIDUE CA C 203
4
AC4
SOFTWARE
HOH C:207 , ASP D:32 , ASP D:34 , ASP D:125 , PO4 D:205 , HOH D:209
BINDING SITE FOR RESIDUE CA D 204
5
BC8
SOFTWARE
ASP A:32 , VAL A:33 , ASP A:34 , THR A:76 , GLY A:77 , LYS A:102 , CA A:201 , HOH A:203 , HOH A:204 , HOH A:205 , SER D:187
BINDING SITE FOR RESIDUE PO4 A 202
6
BC9
SOFTWARE
SER A:187 , ASP B:32 , VAL B:33 , ASP B:34 , THR B:76 , GLY B:77 , LYS B:102 , CA B:202 , HOH B:206
BINDING SITE FOR RESIDUE PO4 B 203
7
CC1
SOFTWARE
SER B:187 , HOH B:207 , ASP C:32 , VAL C:33 , ASP C:34 , THR C:76 , GLY C:77 , LYS C:102 , CA C:203 , HOH C:205 , HOH C:206
BINDING SITE FOR RESIDUE PO4 C 204
8
CC2
SOFTWARE
SER C:187 , ASP D:32 , VAL D:33 , ASP D:34 , THR D:76 , GLY D:77 , LYS D:102 , CA D:204 , HOH D:209 , HOH D:210
BINDING SITE FOR RESIDUE PO4 D 205
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d2r8za_ (A:)
1b: SCOP_d2r8zc_ (C:)
1c: SCOP_d2r8zd_ (D:)
1d: SCOP_d2r8ze_ (E:)
1e: SCOP_d2r8zf_ (F:)
1f: SCOP_d2r8zg_ (G:)
1g: SCOP_d2r8zh_ (H:)
1h: SCOP_d2r8zi_ (I:)
1i: SCOP_d2r8zj_ (J:)
1j: SCOP_d2r8zk_ (K:)
1k: SCOP_d2r8zl_ (L:)
1l: SCOP_d2r8zm_ (M:)
1m: SCOP_d2r8zn_ (N:)
1n: SCOP_d2r8zo_ (O:)
1o: SCOP_d2r8zp_ (P:)
1p: SCOP_d2r8zb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
automated matches
(99)
Protein domain
:
automated matches
(99)
Escherichia coli [TaxId: 217992]
(2)
1a
d2r8za_
A:
1b
d2r8zc_
C:
1c
d2r8zd_
D:
1d
d2r8ze_
E:
1e
d2r8zf_
F:
1f
d2r8zg_
G:
1g
d2r8zh_
H:
1h
d2r8zi_
I:
1i
d2r8zj_
J:
1j
d2r8zk_
K:
1k
d2r8zl_
L:
1l
d2r8zm_
M:
1m
d2r8zn_
N:
1n
d2r8zo_
O:
1o
d2r8zp_
P:
1p
d2r8zb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Hydrolase_3_2r8zP01 (P:88-167)
1b: PFAM_Hydrolase_3_2r8zP02 (P:88-167)
1c: PFAM_Hydrolase_3_2r8zP03 (P:88-167)
1d: PFAM_Hydrolase_3_2r8zP04 (P:88-167)
1e: PFAM_Hydrolase_3_2r8zP05 (P:88-167)
1f: PFAM_Hydrolase_3_2r8zP06 (P:88-167)
1g: PFAM_Hydrolase_3_2r8zP07 (P:88-167)
1h: PFAM_Hydrolase_3_2r8zP08 (P:88-167)
1i: PFAM_Hydrolase_3_2r8zP09 (P:88-167)
1j: PFAM_Hydrolase_3_2r8zP10 (P:88-167)
1k: PFAM_Hydrolase_3_2r8zP11 (P:88-167)
1l: PFAM_Hydrolase_3_2r8zP12 (P:88-167)
1m: PFAM_Hydrolase_3_2r8zP13 (P:88-167)
1n: PFAM_Hydrolase_3_2r8zP14 (P:88-167)
1o: PFAM_Hydrolase_3_2r8zP15 (P:88-167)
1p: PFAM_Hydrolase_3_2r8zP16 (P:88-167)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase_3
(28)
Escherichia coli O6
(4)
1a
Hydrolase_3-2r8zP01
P:88-167
1b
Hydrolase_3-2r8zP02
P:88-167
1c
Hydrolase_3-2r8zP03
P:88-167
1d
Hydrolase_3-2r8zP04
P:88-167
1e
Hydrolase_3-2r8zP05
P:88-167
1f
Hydrolase_3-2r8zP06
P:88-167
1g
Hydrolase_3-2r8zP07
P:88-167
1h
Hydrolase_3-2r8zP08
P:88-167
1i
Hydrolase_3-2r8zP09
P:88-167
1j
Hydrolase_3-2r8zP10
P:88-167
1k
Hydrolase_3-2r8zP11
P:88-167
1l
Hydrolase_3-2r8zP12
P:88-167
1m
Hydrolase_3-2r8zP13
P:88-167
1n
Hydrolase_3-2r8zP14
P:88-167
1o
Hydrolase_3-2r8zP15
P:88-167
1p
Hydrolase_3-2r8zP16
P:88-167
[
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
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 (493 KB)
Header - Asym.Unit
Biol.Unit 1 (239 KB)
Header - Biol.Unit 1
Biol.Unit 2 (252 KB)
Header - Biol.Unit 2
Biol.Unit 3 (131 KB)
Header - Biol.Unit 3
Biol.Unit 4 (124 KB)
Header - Biol.Unit 4
Biol.Unit 5 (130 KB)
Header - Biol.Unit 5
Biol.Unit 6 (123 KB)
Header - Biol.Unit 6
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
2R8Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
