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1D5R
Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PTEN TUMOR SUPPRESSOR
Authors
:
J. O. Lee, H. Yang, M. -M. Georgescu, A. Di Cristofano, N. P. Pavletich
Date
:
11 Oct 99 (Deposition) - 04 Nov 99 (Release) - 24 Feb 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
C2 Domain, Phosphotidylinositol, Phosphatase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. O. Lee, H. Yang, M. M. Georgescu, A. Di Cristofano, T. Maehama, Y. Shi, J. E. Dixon, P. Pandolfi, N. P. Pavletich
Crystal Structure Of The Pten Tumor Suppressor: Implication For Its Phosphoinositide Phosphatase Activity And Membrane Association.
Cell(Cambridge, Mass. ) V. 99 323 1999
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: L(+)-TARTARIC ACID (TLAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TLA
1
Ligand/Ion
L(+)-TARTARIC ACID
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:92 , HIS A:93 , CYS A:124 , LYS A:125 , ALA A:126 , GLY A:129 , ARG A:130 , GLN A:171 , HOH A:1381 , HOH A:1439
BINDING SITE FOR RESIDUE TLA A 1352
[
close Site info
]
SAPs(SNPs)/Variants
(69, 69)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_007457 (R15S, chain A, )
02: VAR_026249 (Y16C, chain A, )
03: VAR_018100 (D19N, chain A, )
04: VAR_026250 (G20E, chain A, )
05: VAR_026251 (Y27S, chain A, )
06: VAR_008734 (A34D, chain A, )
07: VAR_008036 (M35R, chain A, )
08: VAR_007458 (G36E, chain A, )
09: VAR_026252 (G36R, chain A, )
10: VAR_007459 (L42R, chain A, )
11: VAR_011587 (R47G, chain A, )
12: VAR_007460 (L57W, chain A, )
13: VAR_018101 (H61D, chain A, )
14: VAR_026253 (H61R, chain A, )
15: VAR_007461 (I67R, chain A, )
16: VAR_007462 (Y68H, chain A, )
17: VAR_018102 (L70P, chain A, )
18: VAR_026254 (C71Y, chain A, )
19: VAR_032634 (H93R, chain A, )
20: VAR_026255 (H93Y, chain A, )
21: VAR_026256 (C105F, chain A, )
22: VAR_008735 (C105Y, chain A, )
23: VAR_026257 (D107Y, chain A, )
24: VAR_007807 (L112P, chain A, )
25: VAR_026258 (L112R, chain A, )
26: VAR_011588 (V119L, chain A, )
27: VAR_018103 (A121G, chain A, )
28: VAR_026259 (A121P, chain A, )
29: VAR_007463 (H123R, chain A, )
30: VAR_026260 (H123Y, chain A, )
31: VAR_007464 (C124R, chain A, )
32: VAR_018104 (C124S, chain A, )
33: VAR_007465 (G129E, chain A, )
34: VAR_007466 (G129R, chain A, )
35: VAR_026261 (R130G, chain A, )
36: VAR_007467 (R130L, chain A, )
37: VAR_007468 (R130Q, chain A, )
38: VAR_032635 (G132V, chain A, )
39: VAR_026262 (V133I, chain A, )
40: VAR_007469 (M134L, chain A, )
41: VAR_008736 (I135V, chain A, )
42: VAR_007808 (C136Y, chain A, )
43: VAR_026263 (Y155C, chain A, )
44: VAR_011589 (V158L, chain A, )
45: VAR_008739 (G165E, chain A, )
46: VAR_026264 (G165R, chain A, )
47: VAR_008738 (G165V, chain A, )
48: VAR_026265 (T167P, chain A, )
49: VAR_026266 (S170N, chain A, )
50: VAR_007470 (S170R, chain A, )
51: VAR_026267 (R173C, chain A, )
52: VAR_026268 (R173H, chain A, )
53: VAR_026269 (R173P, chain A, )
54: VAR_026270 (Y174N, chain A, )
55: VAR_026271 (V191A, chain A, )
56: VAR_018105 (V217I, chain A, )
57: VAR_026272 (S227F, chain A, )
58: VAR_018106 (R234Q, chain A, )
59: VAR_032636 (F241S, chain A, )
60: VAR_008740 (P246L, chain A, )
61: VAR_026273 (G251C, chain A, )
62: VAR_032637 (D252G, chain A, )
63: VAR_026275 (D331G, chain A, )
64: VAR_026276 (F341V, chain A, )
65: VAR_026277 (K342N, chain A, )
66: VAR_008742 (V343E, chain A, )
67: VAR_026278 (L345Q, chain A, )
68: VAR_008743 (F347L, chain A, )
69: VAR_026279 (T348I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_007457
R
15
S
PTEN_HUMAN
Unclassified
---
A
R
15
S
02
UniProt
VAR_026249
Y
16
C
PTEN_HUMAN
Unclassified
---
A
Y
16
C
03
UniProt
VAR_018100
D
19
N
PTEN_HUMAN
Unclassified
---
A
D
19
N
04
UniProt
VAR_026250
G
20
E
PTEN_HUMAN
Unclassified
---
A
G
20
E
05
UniProt
VAR_026251
Y
27
S
PTEN_HUMAN
Unclassified
---
A
Y
27
S
06
UniProt
VAR_008734
A
34
D
PTEN_HUMAN
Disease (BRRS)
---
A
A
34
D
07
UniProt
VAR_008036
M
35
R
PTEN_HUMAN
Disease (CWS1)
---
A
M
35
R
08
UniProt
VAR_007458
G
36
E
PTEN_HUMAN
Unclassified
---
A
G
36
E
09
UniProt
VAR_026252
G
36
R
PTEN_HUMAN
Unclassified
---
A
G
36
R
10
UniProt
VAR_007459
L
42
R
PTEN_HUMAN
Unclassified
---
A
L
42
R
11
UniProt
VAR_011587
R
47
G
PTEN_HUMAN
Disease (CWS1)
---
A
R
47
G
12
UniProt
VAR_007460
L
57
W
PTEN_HUMAN
Unclassified
---
A
L
57
W
13
UniProt
VAR_018101
H
61
D
PTEN_HUMAN
Unclassified
---
A
H
61
D
14
UniProt
VAR_026253
H
61
R
PTEN_HUMAN
Unclassified
---
A
H
61
R
15
UniProt
VAR_007461
I
67
R
PTEN_HUMAN
Disease (CWS1)
---
A
I
67
R
16
UniProt
VAR_007462
Y
68
H
PTEN_HUMAN
Disease (CWS1)
---
A
Y
68
H
17
UniProt
VAR_018102
L
70
P
PTEN_HUMAN
Disease (CWS1)
---
A
L
70
P
18
UniProt
VAR_026254
C
71
Y
PTEN_HUMAN
Disease (CWS1)
---
A
C
71
Y
19
UniProt
VAR_032634
H
93
R
PTEN_HUMAN
Disease (MCEPHAS)
---
A
H
93
R
20
UniProt
VAR_026255
H
93
Y
PTEN_HUMAN
Disease (CWS1)
---
A
H
93
Y
21
UniProt
VAR_026256
C
105
F
PTEN_HUMAN
Disease (BRRS)
---
A
C
105
F
22
UniProt
VAR_008735
C
105
Y
PTEN_HUMAN
Disease (BRRS)
---
A
C
105
Y
23
UniProt
VAR_026257
D
107
Y
PTEN_HUMAN
Disease (BRRS)
---
A
D
107
Y
24
UniProt
VAR_007807
L
112
P
PTEN_HUMAN
Disease (LDD)
---
A
L
112
P
25
UniProt
VAR_026258
L
112
R
PTEN_HUMAN
Unclassified
---
A
L
112
R
26
UniProt
VAR_011588
V
119
L
PTEN_HUMAN
Unclassified
---
A
V
119
L
27
UniProt
VAR_018103
A
121
G
PTEN_HUMAN
Disease (HNSCC)
---
A
A
121
G
28
UniProt
VAR_026259
A
121
P
PTEN_HUMAN
Unclassified
---
A
A
121
P
29
UniProt
VAR_007463
H
123
R
PTEN_HUMAN
Disease (CWS1)
---
A
H
123
R
30
UniProt
VAR_026260
H
123
Y
PTEN_HUMAN
Disease (ENDMC)
---
A
H
123
Y
31
UniProt
VAR_007464
C
124
R
PTEN_HUMAN
Disease (CWS1)
---
A
C
124
R
32
UniProt
VAR_018104
C
124
S
PTEN_HUMAN
Disease (CWS1)
---
A
C
124
S
33
UniProt
VAR_007465
G
129
E
PTEN_HUMAN
Disease (CWS1)
---
A
G
129
E
34
UniProt
VAR_007466
G
129
R
PTEN_HUMAN
Unclassified
---
A
G
129
R
35
UniProt
VAR_026261
R
130
G
PTEN_HUMAN
Unclassified
---
A
R
130
G
36
UniProt
VAR_007467
R
130
L
PTEN_HUMAN
Disease (CWS1)
---
A
R
130
L
37
UniProt
VAR_007468
R
130
Q
PTEN_HUMAN
Disease (CWS1)
---
A
R
130
Q
38
UniProt
VAR_032635
G
132
V
PTEN_HUMAN
Unclassified
---
A
G
132
V
39
UniProt
VAR_026262
V
133
I
PTEN_HUMAN
Unclassified
---
A
V
133
I
40
UniProt
VAR_007469
M
134
L
PTEN_HUMAN
Disease (PC)
---
A
M
134
L
41
UniProt
VAR_008736
I
135
V
PTEN_HUMAN
Disease (BRRS)
---
A
I
135
V
42
UniProt
VAR_007808
C
136
Y
PTEN_HUMAN
Disease (CWS1)
---
A
C
136
Y
43
UniProt
VAR_026263
Y
155
C
PTEN_HUMAN
Disease (CWS1)
---
A
Y
155
C
44
UniProt
VAR_011589
V
158
L
PTEN_HUMAN
Unclassified
---
A
V
158
L
45
UniProt
VAR_008739
G
165
E
PTEN_HUMAN
Disease (CWS1)
---
A
G
165
E
46
UniProt
VAR_026264
G
165
R
PTEN_HUMAN
Unclassified
---
A
G
165
R
47
UniProt
VAR_008738
G
165
V
PTEN_HUMAN
Disease (CWS1)
---
A
G
165
V
48
UniProt
VAR_026265
T
167
P
PTEN_HUMAN
Unclassified
---
A
T
167
P
49
UniProt
VAR_026266
S
170
N
PTEN_HUMAN
Unclassified
---
A
S
170
N
50
UniProt
VAR_007470
S
170
R
PTEN_HUMAN
Disease (BRRS)
---
A
S
170
R
51
UniProt
VAR_026267
R
173
C
PTEN_HUMAN
Unclassified
---
A
R
173
C
52
UniProt
VAR_026268
R
173
H
PTEN_HUMAN
Unclassified
---
A
R
173
H
53
UniProt
VAR_026269
R
173
P
PTEN_HUMAN
Unclassified
---
A
R
173
P
54
UniProt
VAR_026270
Y
174
N
PTEN_HUMAN
Unclassified
---
A
Y
174
N
55
UniProt
VAR_026271
V
191
A
PTEN_HUMAN
Unclassified
---
A
V
191
A
56
UniProt
VAR_018105
V
217
I
PTEN_HUMAN
Unclassified
---
A
V
217
I
57
UniProt
VAR_026272
S
227
F
PTEN_HUMAN
Unclassified
---
A
S
227
F
58
UniProt
VAR_018106
R
234
Q
PTEN_HUMAN
Disease (GLM2)
---
A
R
234
Q
59
UniProt
VAR_032636
F
241
S
PTEN_HUMAN
Disease (MCEPHAS)
---
A
F
241
S
60
UniProt
VAR_008740
P
246
L
PTEN_HUMAN
Disease (CWS1)
---
A
P
246
L
61
UniProt
VAR_026273
G
251
C
PTEN_HUMAN
Unclassified
---
A
G
251
C
62
UniProt
VAR_032637
D
252
G
PTEN_HUMAN
Disease (MCEPHAS)
---
A
D
252
G
63
UniProt
VAR_026275
D
331
G
PTEN_HUMAN
Disease (CWS1)
---
A
D
331
G
64
UniProt
VAR_026276
F
341
V
PTEN_HUMAN
Disease (CWS1)
---
A
F
341
V
65
UniProt
VAR_026277
K
342
N
PTEN_HUMAN
Disease (CWS1)
---
A
K
342
N
66
UniProt
VAR_008742
V
343
E
PTEN_HUMAN
Disease (CWS1)
---
A
V
343
E
67
UniProt
VAR_026278
L
345
Q
PTEN_HUMAN
Unclassified
---
A
L
345
Q
68
UniProt
VAR_008743
F
347
L
PTEN_HUMAN
Disease (CWS1)
---
A
F
347
L
69
UniProt
VAR_026279
T
348
I
PTEN_HUMAN
Unclassified
---
A
T
348
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PPASE_TENSIN (A:14-185)
2: C2_TENSIN (A:190-350)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PPASE_TENSIN
PS51181
Phosphatase tensin-type domain profile.
PTEN_HUMAN
14-185
1
A:14-185
2
C2_TENSIN
PS51182
C2 tensin-type domain profile.
PTEN_HUMAN
190-350
1
A:190-350
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.1a (A:14-27)
Exon 1.3a (A:27-55)
Exon 1.4a (A:55-70)
Exon 1.5 (A:70-85)
Exon 1.6a (A:85-164)
Exon 1.7a (A:165-212)
Exon 1.8 (A:212-267)
Exon 1.9a (A:268-342 (gaps))
Exon 1.10 (A:343-351)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.3a
03: Boundary 1.3a/1.4a
04: Boundary 1.4a/1.5
05: Boundary 1.5/1.6a
06: Boundary 1.6a/1.7a
07: Boundary 1.7a/1.8
08: Boundary 1.8/1.9a
09: Boundary 1.9a/1.10
10: Boundary 1.10/-
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
1.1a
ENST00000371953
1a
ENSE00001456562
chr10:
89622870-89624305
1436
PTEN_HUMAN
1-27
27
1
A:14-27
14
1.3a
ENST00000371953
3a
ENSE00001156351
chr10:
89653782-89653866
85
PTEN_HUMAN
27-55
29
1
A:27-55
29
1.4a
ENST00000371953
4a
ENSE00001156344
chr10:
89685270-89685314
45
PTEN_HUMAN
55-70
16
1
A:55-70
16
1.5
ENST00000371953
5
ENSE00001156337
chr10:
89690803-89690846
44
PTEN_HUMAN
70-85
16
1
A:70-85
16
1.6a
ENST00000371953
6a
ENSE00001156330
chr10:
89692770-89693008
239
PTEN_HUMAN
85-164
80
1
A:85-164
80
1.7a
ENST00000371953
7a
ENSE00001156327
chr10:
89711875-89712016
142
PTEN_HUMAN
165-212
48
1
A:165-212
48
1.8
ENST00000371953
8
ENSE00001156321
chr10:
89717610-89717776
167
PTEN_HUMAN
212-267
56
1
A:212-267
56
1.9a
ENST00000371953
9a
ENSE00001156315
chr10:
89720651-89720875
225
PTEN_HUMAN
268-342
75
1
A:268-342 (gaps)
75
1.10
ENST00000371953
10
ENSE00001456541
chr10:
89725044-89731687
6644
PTEN_HUMAN
343-403
61
1
A:343-351
9
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1d5ra1 (A:188-351)
2a: SCOP_d1d5ra2 (A:14-187)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
C2 domain-like
(198)
Superfamily
:
C2 domain (Calcium/lipid-binding domain, CaLB)
(148)
Family
:
PLC-like (P variant)
(81)
Protein domain
:
Pten tumor suppressor (Phoshphoinositide phosphatase), C-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1d5ra1
A:188-351
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
(Phosphotyrosine protein) phosphatases II
(296)
Superfamily
:
(Phosphotyrosine protein) phosphatases II
(296)
Family
:
Dual specificity phosphatase-like
(27)
Protein domain
:
Phoshphoinositide phosphatase Pten (Pten tumor suppressor), N-terminal domain
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1d5ra2
A:14-187
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1d5rA01 (A:14-187)
2a: CATH_1d5rA02 (A:188-351)
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
1d5rA01
A:14-187
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1110, no name defined]
(1)
Human (Homo sapiens)
(1)
2a
1d5rA02
A:188-351
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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
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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)
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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") .
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Asym.Unit (66 KB)
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