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.
2OOQ
Biol. Unit 2
Info
Asym.Unit (107 KB)
Biol.Unit 1 (50 KB)
Biol.Unit 2 (54 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 THE HUMAN RECEPTOR PHOSPHATASE PTPRT
Authors
:
E. Ugochukwu, I. Alfano, A. Barr, T. Keates, J. Eswaran, E. Salah, P. Sav G. Bunkoczi, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, F Delft, S. Knapp, Structural Genomics Consortium (Sgc)
Date
:
26 Jan 07 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein Tyrosine Phosphatase, Receptor, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Muller, S. Knapp
Large-Scale Structural Analysis Of The Classical Human Protein Tyrosine Phosphatome.
Cell(Cambridge, Mass. ) V. 136 352 2009
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
1b: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pb)
2a: 1,2-ETHANEDIOL (EDOa)
3a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B3P
1
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:978 , ILE B:1102 , ASP B:1120
BINDING SITE FOR RESIDUE NA B 501
2
AC3
SOFTWARE
GLU B:1039 , GLU B:1041 , THR B:1050 , ARG B:1065 , HOH B:1191 , HOH B:1256 , HOH B:1371 , HOH B:1390 , HOH B:1439 , HOH B:1441
BINDING SITE FOR RESIDUE B3P B 301
3
AC4
SOFTWARE
TRP B:1072 , GLY B:1076 , ARG B:1112 , GLN B:1154 , HOH B:1229 , HOH B:1301 , HOH B:1442
BINDING SITE FOR RESIDUE EDO B 502
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_020761 (D927G, chain B, )
2: VAR_020762 (Q987K, chain B, )
3: VAR_020763 (A1118P, chain B, )
4: VAR_020764 (N1128I, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020761
D
905
G
PTPRT_HUMAN
Unclassified
---
B
D
927
G
2
UniProt
VAR_020762
Q
965
K
PTPRT_HUMAN
Unclassified
---
B
Q
987
K
3
UniProt
VAR_020763
A
1096
P
PTPRT_HUMAN
Unclassified
---
B
A
1118
P
4
UniProt
VAR_020764
N
1106
I
PTPRT_HUMAN
Unclassified
---
B
N
1128
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TYR_PHOSPHATASE_PTP (B:911-1165|-)
2: TYR_PHOSPHATASE_2 (B:1085-1156|-)
3: TYR_PHOSPHATASE_1 (B:1104-1114|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TYR_PHOSPHATASE_PTP
PS50055
PTP type protein phosphatase family profile.
PTPRT_HUMAN
889-1143
1175-1437
1
-
B:911-1165
-
2
TYR_PHOSPHATASE_2
PS50056
Tyrosine specific protein phosphatases family profile.
PTPRT_HUMAN
1063-1134
1351-1428
1
-
B:1085-1156
-
3
TYR_PHOSPHATASE_1
PS00383
Tyrosine specific protein phosphatases active site.
PTPRT_HUMAN
1082-1092
1376-1386
1
-
B:1104-1114
-
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d2ooqa_ (A:)
1b: SCOP_d2ooqb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
(Phosphotyrosine protein) phosphatases II
(296)
Superfamily
:
(Phosphotyrosine protein) phosphatases II
(296)
Family
:
Higher-molecular-weight phosphotyrosine protein phosphatases
(166)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d2ooqa_
A:
1b
d2ooqb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2ooqA00 (A:889-1168)
1b: CATH_2ooqB00 (B:888-1168)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Protein-Tyrosine Phosphatase; Chain A
(262)
Homologous Superfamily
:
Protein tyrosine phosphatase superfamily
(228)
Human (Homo sapiens)
(196)
1a
2ooqA00
A:889-1168
1b
2ooqB00
B:888-1168
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Y_phosphatase_2ooqB01 (B:934-1164)
1b: PFAM_Y_phosphatase_2ooqB02 (B:934-1164)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Phosphatase
(121)
Family
:
Y_phosphatase
(93)
Homo sapiens (Human)
(82)
1a
Y_phosphatase-2ooqB01
B:934-1164
1b
Y_phosphatase-2ooqB02
B:934-1164
[
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 B
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 (107 KB)
Header - Asym.Unit
Biol.Unit 1 (50 KB)
Header - Biol.Unit 1
Biol.Unit 2 (54 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
2OOQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
