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4CMN
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (119 KB)
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Title
:
CRYSTAL STRUCTURE OF OCRL IN COMPLEX WITH A PHOSPHATE ION
Authors
:
L. Tresaugues, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, A. M T. Ekblad, S. Flodin, S. Graslund, T. Karlberg, T. Nyman, H. Schuler, C. Silvander, A. G. Thorsell, J. Weigelt, M. Welin, P. Nordlund
Date
:
16 Jan 14 (Deposition) - 16 Apr 14 (Release) - 21 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.13
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Inositol Signalling, Sgc Stockholm, Structural Genomics Consortium, Lowe Syndrome, Dent Disease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Tresaugues, C. Silvander, S. Flodin, M. Welin, T. Nyman, S. Graslund, M. Hammarstrom, H. Berglund, P. Nordlund
Structural Basis For Phosphoinositide Substrate Recognition, Catalysis, And Membrane Interactions In Human Inositol Polyphosphate 5-Phosphatases.
Structure V. 22 744 2014
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: MAGNESIUM ION (MGa)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
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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
ASN A:248 , GLU A:278 , TYR A:477 , ASP A:523 , HIS A:524 , MG A:1561 , HOH A:2002
BINDING SITE FOR RESIDUE PO4 A1560
2
AC2
SOFTWARE
ASN A:250 , GLU A:278 , PO4 A:1560
BINDING SITE FOR RESIDUE MG A1561
3
AC3
SOFTWARE
LYS A:229 , ASN A:354 , LYS A:355 , HIS A:379
BINDING SITE FOR RESIDUE GOL A1562
4
AC4
SOFTWARE
ASN A:454 , ARG A:457 , THR A:458
BINDING SITE FOR RESIDUE GOL A1563
[
close Site info
]
SAPs(SNPs)/Variants
(37, 37)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_064773 (F242S, chain A, )
02: VAR_064774 (I274T, chain A, )
03: VAR_064775 (Q277R, chain A, )
04: VAR_022698 (R318C, chain A, )
05: VAR_064776 (R337C, chain A, )
06: VAR_010169 (R337P, chain A, )
07: VAR_064777 (N354H, chain A, )
08: VAR_010170 (G357E, chain A, )
09: VAR_064778 (R361I, chain A, )
10: VAR_010172 (V372G, chain A, )
11: VAR_064779 (N373Y, chain A, )
12: VAR_064780 (S374F, chain A, )
13: VAR_010173 (H375Y, chain A, )
14: VAR_064781 (H414R, chain A, )
15: VAR_010174 (G421E, chain A, )
16: VAR_010175 (N424D, chain A, )
17: VAR_010176 (D451G, chain A, )
18: VAR_064782 (D451N, chain A, )
19: VAR_064783 (R457G, chain A, )
20: VAR_010177 (F463S, chain A, )
21: VAR_064784 (E468G, chain A, )
22: VAR_064785 (E468K, chain A, )
23: VAR_022699 (Y479C, chain A, )
24: VAR_064786 (R493W, chain A, )
25: VAR_064787 (P495L, chain A, )
26: VAR_010178 (C498Y, chain A, )
27: VAR_064788 (D499H, chain A, )
28: VAR_010179 (R500G, chain A, )
29: VAR_010180 (R500Q, chain A, )
30: VAR_064789 (W503R, chain A, )
31: VAR_010181 (V508D, chain A, )
32: VAR_010182 (Y513C, chain A, )
33: VAR_010183 (S522R, chain A, )
34: VAR_010184 (H524Q, chain A, )
35: VAR_010185 (H524R, chain A, )
36: VAR_023958 (P526L, chain A, )
37: VAR_010187 (I533S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_064773
F
242
S
OCRL_HUMAN
Disease (OCRL)
137853828
A
F
242
S
02
UniProt
VAR_064774
I
274
T
OCRL_HUMAN
Disease (OCRL)
137853829
A
I
274
T
03
UniProt
VAR_064775
Q
277
R
OCRL_HUMAN
Disease (OCRL)
137853830
A
Q
277
R
04
UniProt
VAR_022698
R
318
C
OCRL_HUMAN
Disease (OCRL)
137853263
A
R
318
C
05
UniProt
VAR_064776
R
337
C
OCRL_HUMAN
Disease (OCRL)
137853831
A
R
337
C
06
UniProt
VAR_010169
R
337
P
OCRL_HUMAN
Disease (OCRL)
---
A
R
337
P
07
UniProt
VAR_064777
N
354
H
OCRL_HUMAN
Disease (DD2)
137853833
A
N
354
H
08
UniProt
VAR_010170
G
357
E
OCRL_HUMAN
Unclassified
137853854
A
G
357
E
09
UniProt
VAR_064778
R
361
I
OCRL_HUMAN
Disease (OCRL)
137853832
A
R
361
I
10
UniProt
VAR_010172
V
372
G
OCRL_HUMAN
Disease (OCRL)
137853834
A
V
372
G
11
UniProt
VAR_064779
N
373
Y
OCRL_HUMAN
Disease (OCRL)
137853835
A
N
373
Y
12
UniProt
VAR_064780
S
374
F
OCRL_HUMAN
Disease (OCRL)
137853836
A
S
374
F
13
UniProt
VAR_010173
H
375
Y
OCRL_HUMAN
Disease (OCRL)
137853848
A
H
375
Y
14
UniProt
VAR_064781
H
414
R
OCRL_HUMAN
Disease (OCRL)
137853837
A
H
414
R
15
UniProt
VAR_010174
G
421
E
OCRL_HUMAN
Disease (OCRL)
137853855
A
G
421
E
16
UniProt
VAR_010175
N
424
D
OCRL_HUMAN
Disease (OCRL)
137853856
A
N
424
D
17
UniProt
VAR_010176
D
451
G
OCRL_HUMAN
Disease (OCRL)
137853850
A
D
451
G
18
UniProt
VAR_064782
D
451
N
OCRL_HUMAN
Disease (OCRL)
137853838
A
D
451
N
19
UniProt
VAR_064783
R
457
G
OCRL_HUMAN
Disease (OCRL)
137853839
A
R
457
G
20
UniProt
VAR_010177
F
463
S
OCRL_HUMAN
Disease (OCRL)
137853851
A
F
463
S
21
UniProt
VAR_064784
E
468
G
OCRL_HUMAN
Disease (OCRL)
137853841
A
E
468
G
22
UniProt
VAR_064785
E
468
K
OCRL_HUMAN
Disease (OCRL)
137853840
A
E
468
K
23
UniProt
VAR_022699
Y
479
C
OCRL_HUMAN
Disease (DD2)
137853262
A
Y
479
C
24
UniProt
VAR_064786
R
493
W
OCRL_HUMAN
Disease (DD2)
137853846
A
R
493
W
25
UniProt
VAR_064787
P
495
L
OCRL_HUMAN
Disease (OCRL)
---
A
P
495
L
26
UniProt
VAR_010178
C
498
Y
OCRL_HUMAN
Disease (OCRL)
137853857
A
C
498
Y
27
UniProt
VAR_064788
D
499
H
OCRL_HUMAN
Disease (OCRL)
137853842
A
D
499
H
28
UniProt
VAR_010179
R
500
G
OCRL_HUMAN
Disease (OCRL)
---
A
R
500
G
29
UniProt
VAR_010180
R
500
Q
OCRL_HUMAN
Disease (OCRL)
137853260
A
R
500
Q
30
UniProt
VAR_064789
W
503
R
OCRL_HUMAN
Disease (OCRL)
137853843
A
W
503
R
31
UniProt
VAR_010181
V
508
D
OCRL_HUMAN
Disease (OCRL)
137853849
A
V
508
D
32
UniProt
VAR_010182
Y
513
C
OCRL_HUMAN
Disease (OCRL)
137853847
A
Y
513
C
33
UniProt
VAR_010183
S
522
R
OCRL_HUMAN
Disease (OCRL)
137853853
A
S
522
R
34
UniProt
VAR_010184
H
524
Q
OCRL_HUMAN
Disease (OCRL)
137853261
A
H
524
Q
35
UniProt
VAR_010185
H
524
R
OCRL_HUMAN
Disease (OCRL)
137853852
A
H
524
R
36
UniProt
VAR_023958
P
526
L
OCRL_HUMAN
Disease (OCRL)
137853858
A
P
526
L
37
UniProt
VAR_010187
I
533
S
OCRL_HUMAN
Disease (OCRL)
---
A
I
533
S
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
(9, 9)
Info
All Exons
Exon 1.10b (A:219-241)
Exon 1.11 (A:241-275)
Exon 1.12 (A:275-313)
Exon 1.13 (A:314-352)
Exon 1.14 (A:353-415 (gaps))
Exon 1.15 (A:415-452)
Exon 1.16a (A:453-489)
Exon 1.17 (A:489-534)
Exon 1.18 (A:535-559)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.9/1.10b
02: Boundary 1.10b/1.11
03: Boundary 1.11/1.12
04: Boundary 1.12/1.13
05: Boundary 1.13/1.14
06: Boundary 1.14/1.15
07: Boundary 1.15/1.16a
08: Boundary 1.16a/1.17
09: Boundary 1.17/1.18
10: Boundary 1.18/1.19
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
1.2a
ENST00000371113
2a
ENSE00001518494
X:128674252-128674455
204
OCRL_HUMAN
1-13
13
0
-
-
1.3a
ENST00000371113
3a
ENSE00001454376
X:128674721-128674800
80
OCRL_HUMAN
14-40
27
0
-
-
1.4
ENST00000371113
4
ENSE00001613852
X:128678935-128679014
80
OCRL_HUMAN
40-67
28
0
-
-
1.5a
ENST00000371113
5a
ENSE00001633886
X:128682540-128682578
39
OCRL_HUMAN
67-80
14
0
-
-
1.7
ENST00000371113
7
ENSE00000828196
X:128691302-128691412
111
OCRL_HUMAN
80-117
38
0
-
-
1.8
ENST00000371113
8
ENSE00000828195
X:128691838-128691927
90
OCRL_HUMAN
117-147
31
0
-
-
1.9
ENST00000371113
9
ENSE00000828194
X:128692610-128692730
121
OCRL_HUMAN
147-187
41
0
-
-
1.10b
ENST00000371113
10b
ENSE00000828193
X:128692817-128692978
162
OCRL_HUMAN
187-241
55
1
A:219-241
23
1.11
ENST00000371113
11
ENSE00000828192
X:128694527-128694628
102
OCRL_HUMAN
241-275
35
1
A:241-275
35
1.12
ENST00000371113
12
ENSE00000828191
X:128695156-128695270
115
OCRL_HUMAN
275-313
39
1
A:275-313
39
1.13
ENST00000371113
13
ENSE00000828190
X:128696361-128696477
117
OCRL_HUMAN
314-352
39
1
A:314-352
39
1.14
ENST00000371113
14
ENSE00000828189
X:128696576-128696763
188
OCRL_HUMAN
353-415
63
1
A:353-415 (gaps)
63
1.15
ENST00000371113
15
ENSE00000828188
X:128699749-128699860
112
OCRL_HUMAN
415-452
38
1
A:415-452
38
1.16a
ENST00000371113
16a
ENSE00000828187
X:128701231-128701340
110
OCRL_HUMAN
453-489
37
1
A:453-489
37
1.17
ENST00000371113
17
ENSE00001795169
X:128703241-128703376
136
OCRL_HUMAN
489-534
46
1
A:489-534
46
1.18
ENST00000371113
18
ENSE00000828185
X:128709117-128709227
111
OCRL_HUMAN
535-571
37
1
A:535-559
25
1.19
ENST00000371113
19
ENSE00000828184
X:128709874-128710039
166
OCRL_HUMAN
572-627
56
0
-
-
1.20b
ENST00000371113
20b
ENSE00000828183
X:128710294-128710529
236
OCRL_HUMAN
627-705
79
0
-
-
1.21
ENST00000371113
21
ENSE00001454375
X:128718321-128718344
24
OCRL_HUMAN
706-713
8
0
-
-
1.23
ENST00000371113
23
ENSE00000828182
X:128720979-128721095
117
OCRL_HUMAN
714-752
39
0
-
-
1.24
ENST00000371113
24
ENSE00000828181
X:128722156-128722240
85
OCRL_HUMAN
753-781
29
0
-
-
1.25
ENST00000371113
25
ENSE00000828180
X:128722863-128722990
128
OCRL_HUMAN
781-823
43
0
-
-
1.26b
ENST00000371113
26b
ENSE00000828179
X:128723822-128723933
112
OCRL_HUMAN
824-861
38
0
-
-
1.27c
ENST00000371113
27c
ENSE00001170507
X:128724123-128726538
2416
OCRL_HUMAN
861-901
41
0
-
-
[
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SCOP Domains
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
(0, 0)
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all PFAM domains
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