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.
2OOQ
Asym. Unit
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
(3, 4)
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
2
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
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: 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
AC2
SOFTWARE
HOH A:86 , HOH A:294 , GLU A:1039 , GLU A:1041 , THR A:1050 , ARG A:1065
BINDING SITE FOR RESIDUE B3P A 301
3
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
4
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, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020761 (D927G, chain A/B, )
2: VAR_020762 (Q987K, chain A/B, )
3: VAR_020763 (A1118P, chain A/B, )
4: VAR_020764 (N1128I, chain A/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
---
A/B
D
927
G
2
UniProt
VAR_020762
Q
965
K
PTPRT_HUMAN
Unclassified
---
A/B
Q
987
K
3
UniProt
VAR_020763
A
1096
P
PTPRT_HUMAN
Unclassified
---
A/B
A
1118
P
4
UniProt
VAR_020764
N
1106
I
PTPRT_HUMAN
Unclassified
---
A/B
N
1128
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: TYR_PHOSPHATASE_PTP (A:911-1165,B:911-1165|-)
2: TYR_PHOSPHATASE_2 (A:1085-1156,B:1085-1156|-)
3: TYR_PHOSPHATASE_1 (A:1104-1114,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
2
A:911-1165
B:911-1165
-
2
TYR_PHOSPHATASE_2
PS50056
Tyrosine specific protein phosphatases family profile.
PTPRT_HUMAN
1063-1134
1351-1428
2
A:1085-1156
B:1085-1156
-
3
TYR_PHOSPHATASE_1
PS00383
Tyrosine specific protein phosphatases active site.
PTPRT_HUMAN
1082-1092
1376-1386
2
A:1104-1114
B:1104-1114
-
[
close PROSITE info
]
Exons
(9, 18)
Info
All Exons
Exon 1.20a (A:889-916 | B:888-916)
Exon 1.21 (A:917-946 | B:917-946)
Exon 1.22 (A:946-971 (gaps) | B:946-971)
Exon 1.23 (A:972-984 | B:972-984)
Exon 1.24 (A:984-1016 | B:984-1016)
Exon 1.26 (A:1017-1055 | B:1017-1055)
Exon 1.27 (A:1056-1107 | B:1056-1107)
Exon 1.28 (A:1107-1152 | B:1107-1152)
Exon 1.29 (A:1153-1168 | B:1153-1168)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.19b/1.20a
02: Boundary 1.20a/1.21
03: Boundary 1.21/1.22
04: Boundary 1.22/1.23
05: Boundary 1.23/1.24
06: Boundary 1.24/1.26
07: Boundary 1.26/1.27
08: Boundary 1.27/1.28
09: Boundary 1.28/1.29
10: Boundary 1.29/1.30
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
1.1e
ENST00000373187
1e
ENSE00001299020
chr20:
41818373-41818286
88
PTPRT_HUMAN
1-30
30
0
-
-
1.3b
ENST00000373187
3b
ENSE00001127453
chr20:
41514572-41514447
126
PTPRT_HUMAN
30-72
43
0
-
-
1.4
ENST00000373187
4
ENSE00000662140
chr20:
41420106-41419835
272
PTPRT_HUMAN
72-162
91
0
-
-
1.5
ENST00000373187
5
ENSE00001127981
chr20:
41408939-41408858
82
PTPRT_HUMAN
163-190
28
0
-
-
1.6
ENST00000373187
6
ENSE00001320663
chr20:
41400190-41400075
116
PTPRT_HUMAN
190-228
39
0
-
-
1.7
ENST00000373187
7
ENSE00001295075
chr20:
41385276-41385102
175
PTPRT_HUMAN
229-287
59
0
-
-
1.8
ENST00000373187
8
ENSE00001315163
chr20:
41306799-41306506
294
PTPRT_HUMAN
287-385
99
0
-
-
1.9
ENST00000373187
9
ENSE00001305193
chr20:
41101202-41100906
297
PTPRT_HUMAN
385-484
100
0
-
-
1.10
ENST00000373187
10
ENSE00001329888
chr20:
41076969-41076860
110
PTPRT_HUMAN
484-520
37
0
-
-
1.11
ENST00000373187
11
ENSE00001303836
chr20:
40980925-40980724
202
PTPRT_HUMAN
521-588
68
0
-
-
1.12
ENST00000373187
12
ENSE00001322891
chr20:
40979370-40979268
103
PTPRT_HUMAN
588-622
35
0
-
-
1.13
ENST00000373187
13
ENSE00001303056
chr20:
40944636-40944363
274
PTPRT_HUMAN
622-713
92
0
-
-
1.14
ENST00000373187
14
ENSE00001316436
chr20:
40911165-40911129
37
PTPRT_HUMAN
714-726
13
0
-
-
1.16
ENST00000373187
16
ENSE00001291858
chr20:
40877462-40877327
136
PTPRT_HUMAN
726-771
46
0
-
-
1.17
ENST00000373187
17
ENSE00001296212
chr20:
40864898-40864869
30
PTPRT_HUMAN
771-781
11
0
-
-
1.19b
ENST00000373187
19b
ENSE00001324256
chr20:
40828028-40827880
149
PTPRT_HUMAN
781-831
51
0
-
-
1.20a
ENST00000373187
20a
ENSE00001304010
chr20:
40790182-40789992
191
PTPRT_HUMAN
831-894
64
2
A:889-916
B:888-916
28
29
1.21
ENST00000373187
21
ENSE00001320070
chr20:
40770642-40770555
88
PTPRT_HUMAN
895-924
30
2
A:917-946
B:917-946
30
30
1.22
ENST00000373187
22
ENSE00001293417
chr20:
40757470-40757394
77
PTPRT_HUMAN
924-949
26
2
A:946-971 (gaps)
B:946-971
26
26
1.23
ENST00000373187
23
ENSE00001310313
chr20:
40748611-40748575
37
PTPRT_HUMAN
950-962
13
2
A:972-984
B:972-984
13
13
1.24
ENST00000373187
24
ENSE00001289737
chr20:
40747140-40747043
98
PTPRT_HUMAN
962-994
33
2
A:984-1016
B:984-1016
33
33
1.26
ENST00000373187
26
ENSE00001304469
chr20:
40743955-40743839
117
PTPRT_HUMAN
995-1033
39
2
A:1017-1055
B:1017-1055
39
39
1.27
ENST00000373187
27
ENSE00001290774
chr20:
40739127-40738973
155
PTPRT_HUMAN
1034-1085
52
2
A:1056-1107
B:1056-1107
52
52
1.28
ENST00000373187
28
ENSE00001315899
chr20:
40735561-40735426
136
PTPRT_HUMAN
1085-1130
46
2
A:1107-1152
B:1107-1152
46
46
1.29
ENST00000373187
29
ENSE00001298748
chr20:
40733358-40733209
150
PTPRT_HUMAN
1131-1180
50
2
A:1153-1168
B:1153-1168
16
16
1.30
ENST00000373187
30
ENSE00001314457
chr20:
40730937-40730764
174
PTPRT_HUMAN
1181-1238
58
0
-
-
1.31
ENST00000373187
31
ENSE00001304649
chr20:
40727192-40727061
132
PTPRT_HUMAN
1239-1282
44
0
-
-
1.32
ENST00000373187
32
ENSE00001326438
chr20:
40714493-40714368
126
PTPRT_HUMAN
1283-1324
42
0
-
-
1.33
ENST00000373187
33
ENSE00001299388
chr20:
40713485-40713322
164
PTPRT_HUMAN
1325-1379
55
0
-
-
1.34
ENST00000373187
34
ENSE00001317939
chr20:
40710657-40710522
136
PTPRT_HUMAN
1379-1424
46
0
-
-
1.35b
ENST00000373187
35b
ENSE00001302529
chr20:
40709572-40701392
8181
PTPRT_HUMAN
1425-1441
17
0
-
-
[
close EXON info
]
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 A
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
