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Getting 'Hetero Component' information from database.
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Getting 'PROSITE' information from database.
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Getting 'Exon' information from database.
2V5P
Asym. Unit
Info
Asym.Unit (338 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (168 KB)
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(1)
Title
:
COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II
Authors
:
J. Brown, C. Delaine, O. J. Zaccheo, C. Siebold, R. J. Gilbert, G. Van Boxel, A. Denley, J. C. Wallace, A. B. Hassan, B. E. Forbes, E. Y. Jones
Date
:
06 Jul 07 (Deposition) - 11 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Receptor/Glycoprotein, Cation Independent Mannose 6-Phosphate, Membrane, Receptor, Lysosome, Transport, Beta Barrel, Phosphorylation, Fibronectin Type Ii, Insulin-Like Growth Factor, Receptor/Glycoprotein Complex, Polymorphism, Glycoprotein, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Brown, C. Delaine, O. J. Zaccheo, C. Siebold, R. J. Gilbert, G. Van Boxel, A. Denley, J. C. Wallace, A. B. Hassan, B. E. Forbes, E. Y. Jones
Structure And Functional Analysis Of The Igf-Ii/Igf2R Interaction
Embo J. V. 27 265 2008
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:1656 , ASN A:1738 , VAL A:1794
BINDING SITE FOR RESIDUE NAG A2991
2
AC2
SOFTWARE
SER A:1747 , PRO A:1749 , ASN A:1757
BINDING SITE FOR RESIDUE NAG A2992
3
AC3
SOFTWARE
ASN A:1816 , NAG A:2994
BINDING SITE FOR RESIDUE NAG A2993
4
AC4
SOFTWARE
NAG A:2993 , BMA A:2995
BINDING SITE FOR RESIDUE NAG A2994
5
AC5
SOFTWARE
NAG A:2994 , ASP B:1630
BINDING SITE FOR RESIDUE BMA A2995
6
AC6
SOFTWARE
ASN B:1656 , ASN B:1738 , VAL B:1794
BINDING SITE FOR RESIDUE NAG B2991
7
AC7
SOFTWARE
SER B:1747 , PRO B:1749 , ASN B:1757
BINDING SITE FOR RESIDUE NAG B2992
8
AC8
SOFTWARE
NAG A:2994 , ASP B:1630
BINDING SITE FOR RESIDUE BMA A2995
9
AC9
SOFTWARE
ASN B:1816
BINDING SITE FOR RESIDUE NAG B2993
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021312 (G1619G, chain A/B, )
2: VAR_050430 (Q1696R, chain A/B, )
3: VAR_021313 (R1832H, chain A/B, )
4: VAR_021314 (G1860D, chain A/B, )
5: VAR_021315 (I1908M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021312
R
1619
G
MPRI_HUMAN
Polymorphism
629849
A/B
G
1619
G
2
UniProt
VAR_050430
Q
1696
R
MPRI_HUMAN
Polymorphism
11552587
A/B
Q
1696
R
3
UniProt
VAR_021313
R
1832
H
MPRI_HUMAN
Polymorphism
8191904
A/B
R
1832
H
4
UniProt
VAR_021314
G
1860
D
MPRI_HUMAN
Polymorphism
8191905
A/B
G
1860
D
5
UniProt
VAR_021315
I
1908
M
MPRI_HUMAN
Polymorphism
8191908
A/B
I
1908
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: INSULIN (C:46-60,D:46-60)
2: FN2_2 (A:1898-1944,B:1898-1944)
3: FN2_1 (A:1903-1942,B:1903-1942)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INSULIN
PS00262
Insulin family signature.
IGF2_HUMAN
70-84
2
C:46-60
D:46-60
2
FN2_2
PS51092
Fibronectin type-II collagen-binding domain profile.
MPRI_HUMAN
1898-1944
2
A:1898-1944
B:1898-1944
3
FN2_1
PS00023
Fibronectin type-II collagen-binding domain signature.
MPRI_HUMAN
1903-1942
2
A:1903-1942
B:1903-1942
[
close PROSITE info
]
Exons
(11, 22)
Info
All Exons
Exon 1.32 (A:1516-1524 | B:1516-1524)
Exon 1.33 (A:1524-1564 | B:1524-1564)
Exon 1.34a (A:1564-1649 | B:1564-1649)
Exon 1.35a (A:1650-1722 (gaps) | B:1650-1722 (...)
Exon 1.36 (A:1723-1772 (gaps) | B:1723-1772 (...)
Exon 1.37 (A:1773-1826 | B:1773-1826)
Exon 1.38 (A:1827-1896 | B:1827-1896)
Exon 1.39 (A:1896-1945 | B:1896-1945)
Exon 1.40 (A:1945-1990 | B:1945-1990)
Exon 2.8 (C:6-29 | D:6-29)
Exon 2.9b (C:29-63 (gaps) | D:29-63 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.31/1.32
02: Boundary 1.32/1.33
03: Boundary 1.33/1.34a
04: Boundary 1.34a/1.35a
05: Boundary 1.35a/1.36
06: Boundary 1.36/1.37
07: Boundary 1.37/1.38
08: Boundary 1.38/1.39
09: Boundary 1.39/1.40
10: Boundary 1.40/1.41a
11: Boundary 2.7b/2.8
12: Boundary 2.8/2.9b
13: Boundary 2.9b/2.10i
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
1.1
ENST00000356956
1
ENSE00001375794
chr6:
160390131-160390427
297
MPRI_HUMAN
1-50
50
0
-
-
1.2b
ENST00000356956
2b
ENSE00001086779
chr6:
160412216-160412355
140
MPRI_HUMAN
50-97
48
0
-
-
1.3b
ENST00000356956
3b
ENSE00001086761
chr6:
160430042-160430166
125
MPRI_HUMAN
97-138
42
0
-
-
1.4b
ENST00000356956
4b
ENSE00001086760
chr6:
160431719-160431817
99
MPRI_HUMAN
139-171
33
0
-
-
1.5b
ENST00000356956
5b
ENSE00001086769
chr6:
160445604-160445736
133
MPRI_HUMAN
172-216
45
0
-
-
1.6
ENST00000356956
6
ENSE00001086768
chr6:
160448217-160448346
130
MPRI_HUMAN
216-259
44
0
-
-
1.7
ENST00000356956
7
ENSE00001086798
chr6:
160450582-160450687
106
MPRI_HUMAN
259-294
36
0
-
-
1.8
ENST00000356956
8
ENSE00001086791
chr6:
160453583-160453745
163
MPRI_HUMAN
295-349
55
0
-
-
1.9
ENST00000356956
9
ENSE00001086849
chr6:
160453974-160454139
166
MPRI_HUMAN
349-404
56
0
-
-
1.10
ENST00000356956
10
ENSE00001086784
chr6:
160455451-160455554
104
MPRI_HUMAN
404-439
36
0
-
-
1.11
ENST00000356956
11
ENSE00001086790
chr6:
160461592-160461756
165
MPRI_HUMAN
439-494
56
0
-
-
1.12
ENST00000356956
12
ENSE00001086772
chr6:
160464180-160464320
141
MPRI_HUMAN
494-541
48
0
-
-
1.13
ENST00000356956
13
ENSE00001086774
chr6:
160465546-160465689
144
MPRI_HUMAN
541-589
49
0
-
-
1.14a
ENST00000356956
14a
ENSE00001086759
chr6:
160466777-160466914
138
MPRI_HUMAN
589-635
47
0
-
-
1.15
ENST00000356956
15
ENSE00002155529
chr6:
160467530-160467677
148
MPRI_HUMAN
635-684
50
0
-
-
1.16
ENST00000356956
16
ENSE00002192765
chr6:
160468191-160468368
178
MPRI_HUMAN
684-743
60
0
-
-
1.17b
ENST00000356956
17b
ENSE00001086771
chr6:
160468824-160468939
116
MPRI_HUMAN
744-782
39
0
-
-
1.18
ENST00000356956
18
ENSE00001086764
chr6:
160469407-160469575
169
MPRI_HUMAN
782-838
57
0
-
-
1.19a
ENST00000356956
19a
ENSE00001086781
chr6:
160471505-160471684
180
MPRI_HUMAN
839-898
60
0
-
-
1.20b
ENST00000356956
20b
ENSE00001086850
chr6:
160477456-160477557
102
MPRI_HUMAN
899-932
34
0
-
-
1.21
ENST00000356956
21
ENSE00001086860
chr6:
160479055-160479156
102
MPRI_HUMAN
933-966
34
0
-
-
1.22
ENST00000356956
22
ENSE00001086788
chr6:
160479938-160480130
193
MPRI_HUMAN
967-1031
65
0
-
-
1.23
ENST00000356956
23
ENSE00001086789
chr6:
160481579-160481749
171
MPRI_HUMAN
1031-1088
58
0
-
-
1.24
ENST00000356956
24
ENSE00001086861
chr6:
160482535-160482678
144
MPRI_HUMAN
1088-1136
49
0
-
-
1.25
ENST00000356956
25
ENSE00001086780
chr6:
160482785-160482960
176
MPRI_HUMAN
1136-1194
59
0
-
-
1.26
ENST00000356956
26
ENSE00001086796
chr6:
160483564-160483651
88
MPRI_HUMAN
1195-1224
30
0
-
-
1.27
ENST00000356956
27
ENSE00001086799
chr6:
160484447-160484662
216
MPRI_HUMAN
1224-1296
73
0
-
-
1.28
ENST00000356956
28
ENSE00001086848
chr6:
160485433-160485563
131
MPRI_HUMAN
1296-1339
44
0
-
-
1.29
ENST00000356956
29
ENSE00001086767
chr6:
160485836-160485933
98
MPRI_HUMAN
1340-1372
33
0
-
-
1.30
ENST00000356956
30
ENSE00001086793
chr6:
160489281-160489417
137
MPRI_HUMAN
1372-1418
47
0
-
-
1.31
ENST00000356956
31
ENSE00001086846
chr6:
160490900-160491090
191
MPRI_HUMAN
1418-1481
64
0
-
-
1.32
ENST00000356956
32
ENSE00001086762
chr6:
160492942-160493068
127
MPRI_HUMAN
1482-1524
43
2
A:1516-1524
B:1516-1524
9
9
1.33
ENST00000356956
33
ENSE00001086853
chr6:
160493797-160493916
120
MPRI_HUMAN
1524-1564
41
2
A:1524-1564
B:1524-1564
41
41
1.34a
ENST00000356956
34a
ENSE00001086773
chr6:
160494245-160494501
257
MPRI_HUMAN
1564-1649
86
2
A:1564-1649
B:1564-1649
86
86
1.35a
ENST00000356956
35a
ENSE00001086785
chr6:
160494789-160495007
219
MPRI_HUMAN
1650-1722
73
2
A:1650-1722 (gaps)
B:1650-1722 (gaps)
73
73
1.36
ENST00000356956
36
ENSE00001086782
chr6:
160496879-160497028
150
MPRI_HUMAN
1723-1772
50
2
A:1723-1772 (gaps)
B:1723-1772 (gaps)
50
50
1.37
ENST00000356956
37
ENSE00001086863
chr6:
160499233-160499394
162
MPRI_HUMAN
1773-1826
54
2
A:1773-1826
B:1773-1826
54
54
1.38
ENST00000356956
38
ENSE00001086847
chr6:
160500612-160500819
208
MPRI_HUMAN
1827-1896
70
2
A:1827-1896
B:1827-1896
70
70
1.39
ENST00000356956
39
ENSE00001086859
chr6:
160501161-160501307
147
MPRI_HUMAN
1896-1945
50
2
A:1896-1945
B:1896-1945
50
50
1.40
ENST00000356956
40
ENSE00001086855
chr6:
160504982-160505216
235
MPRI_HUMAN
1945-2023
79
2
A:1945-1990
B:1945-1990
46
46
1.41a
ENST00000356956
41a
ENSE00001086858
chr6:
160506027-160506163
137
MPRI_HUMAN
2023-2069
47
0
-
-
1.42
ENST00000356956
42
ENSE00002173935
chr6:
160509065-160509179
115
MPRI_HUMAN
2069-2107
39
0
-
-
1.43
ENST00000356956
43
ENSE00002187746
chr6:
160510139-160510285
147
MPRI_HUMAN
2107-2156
50
0
-
-
1.44a
ENST00000356956
44a
ENSE00001086857
chr6:
160510948-160511135
188
MPRI_HUMAN
2156-2219
64
0
-
-
1.45a
ENST00000356956
45a
ENSE00001086758
chr6:
160517471-160517657
187
MPRI_HUMAN
2219-2281
63
0
-
-
1.46
ENST00000356956
46
ENSE00002180712
chr6:
160523551-160523703
153
MPRI_HUMAN
2281-2332
52
0
-
-
1.47
ENST00000356956
47
ENSE00002196950
chr6:
160524778-160524847
70
MPRI_HUMAN
2332-2355
24
0
-
-
1.48
ENST00000356956
48
ENSE00001405315
chr6:
160525706-160527583
1878
MPRI_HUMAN
2356-2491
136
0
-
-
2.7b
ENST00000381395
7b
ENSE00001488507
chr11:
2158520-2158418
103
IGF2_HUMAN
-
0
0
-
-
2.8
ENST00000381395
8
ENSE00002158068
chr11:
2156759-2156597
163
IGF2_HUMAN
1-53
53
2
C:6-29
D:6-29
24
24
2.9b
ENST00000381395
9b
ENSE00001655181
chr11:
2154895-2154747
149
IGF2_HUMAN
53-102
50
2
C:29-63 (gaps)
D:29-63 (gaps)
35
35
2.10i
ENST00000381395
10i
ENSE00001488587
chr11:
2154453-2150342
4112
IGF2_HUMAN
103-180
78
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2v5pc1 (C:6-63)
1b: SCOP_d2v5pd1 (D:6-63)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Insulin-like
(117)
Superfamily
:
Insulin-like
(117)
Family
:
Insulin-like
(117)
Protein domain
:
Insulin-like growth factor
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
1a
d2v5pc1
C:6-63
1b
d2v5pd1
D:6-63
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 14)
Info
all PFAM domains
1a: PFAM_Insulin_2v5pD01 (D:40-60)
1b: PFAM_Insulin_2v5pD02 (D:40-60)
1c: PFAM_Insulin_2v5pD03 (D:40-60)
1d: PFAM_Insulin_2v5pD04 (D:40-60)
2a: PFAM_CIMR_2v5pB01 (B:1946-1990)
2b: PFAM_CIMR_2v5pB02 (B:1946-1990)
2c: PFAM_CIMR_2v5pB03 (B:1946-1990)
2d: PFAM_CIMR_2v5pB04 (B:1946-1990)
2e: PFAM_CIMR_2v5pB05 (B:1946-1990)
2f: PFAM_CIMR_2v5pB06 (B:1946-1990)
2g: PFAM_CIMR_2v5pB07 (B:1946-1990)
2h: PFAM_CIMR_2v5pB08 (B:1946-1990)
3a: PFAM_fn2_2v5pB09 (B:1903-1942)
3b: PFAM_fn2_2v5pB10 (B:1903-1942)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Insulin
(93)
Family
:
Insulin
(92)
Homo sapiens (Human)
(79)
1a
Insulin-2v5pD01
D:40-60
1b
Insulin-2v5pD02
D:40-60
1c
Insulin-2v5pD03
D:40-60
1d
Insulin-2v5pD04
D:40-60
Clan
:
M6PR
(17)
Family
:
CIMR
(8)
Homo sapiens (Human)
(3)
2a
CIMR-2v5pB01
B:1946-1990
2b
CIMR-2v5pB02
B:1946-1990
2c
CIMR-2v5pB03
B:1946-1990
2d
CIMR-2v5pB04
B:1946-1990
2e
CIMR-2v5pB05
B:1946-1990
2f
CIMR-2v5pB06
B:1946-1990
2g
CIMR-2v5pB07
B:1946-1990
2h
CIMR-2v5pB08
B:1946-1990
Clan
:
no clan defined [family: fn2]
(6)
Family
:
fn2
(6)
Homo sapiens (Human)
(6)
3a
fn2-2v5pB09
B:1903-1942
3b
fn2-2v5pB10
B:1903-1942
[
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
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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") .
QuickSearch:
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Asym.Unit (338 KB)
Header - Asym.Unit
Biol.Unit 1 (167 KB)
Header - Biol.Unit 1
Biol.Unit 2 (168 KB)
Header - Biol.Unit 2
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