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.
2FYL
Asym. Unit
Info
Asym.Unit (52 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HADDOCK MODEL OF THE COMPLEX BETWEEN DOUBLE MODULE OF LRP, CR56, AND FIRST DOMAIN OF RECEPTOR ASSOCIATED PROTEIN, RAP-D1.
Authors
:
G. A. Jensen, O. M. Andersen, A. M. Bonvin, I. Bjerrum-Bohr, M. Etzerodt, C. O'Shea, F. M. Poulsen, B. B. Kragelund
Date
:
08 Feb 06 (Deposition) - 10 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A,B
Keywords
:
Complex, Shift-Mapping, Haddock, Nmr, Interface, Surface Active Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. A. Jensen, O. M. Andersen, A. M. Bonvin, I. Bjerrum-Bohr, M. Etzerodt, C. O'Shea, F. M. Poulsen, B. B. Kragelund
Binding Site Structure Of One Lrp-Rap Complex:Implications For A Common Ligand-Receptor Binding Motif.
J. Mol. Biol. V. 362 700 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP B:22 , THR B:23 , ASP B:25 , ASP B:27 , ASP B:29 , ASP B:35 , GLU B:36
BINDING SITE FOR RESIDUE CA B 83
2
AC2
SOFTWARE
TRP B:63 , ARG B:64 , ASP B:66 , ASP B:70 , ASP B:76 , GLU B:77
BINDING SITE FOR RESIDUE CA B 84
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050660 (N80S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_050660
N
114
S
AMRP_HUMAN
Polymorphism
2228158
A
N
80
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: LDLRA_2 (-|-|-|-|B:4-41|B:44-81|-|-|-|-|-|-...)
2: LDLRA_1 (-|-|-|-|B:17-40|B:58-80|-|-|-|-|-|...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LDLRA_2
PS50068
LDL-receptor class A (LDLRA) domain profile.
LRP1_HUMAN
26-65
71-109
853-891
894-932
935-972
975-1012
1014-1052
1061-1098
1103-1141
1144-1183
2523-2562
2565-2601
2604-2640
2638-2689
2695-2731
2733-2770
2773-2813
2817-2854
2857-2898
2903-2940
3333-3370
3373-3409
3412-3449
3452-3490
3493-3532
3535-3571
3574-3610
3612-3648
3653-3691
3694-3732
3740-3777
2
-
-
-
-
B:4-41
B:44-81
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
LDLRA_1
PS01209
LDL-receptor class A (LDLRA) domain signature.
LRP1_HUMAN
40-64
85-108
866-890
907-931
948-971
989-1011
1027-1051
1075-1097
1118-1140
1159-1182
2537-2561
2578-2600
2617-2639
2708-2730
2746-2769
2787-2812
2830-2853
2917-2939
3346-3369
3426-3448
3466-3489
3507-3531
3548-3570
3587-3609
3625-3647
3709-3731
3754-3776
2
-
-
-
-
B:17-40
B:58-80
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.19 (B:1-2)
Exon 1.20 (B:2-41)
Exon 1.21 (B:41-68)
Exon 1.22 (B:68-82)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.18/1.19
2: Boundary 1.19/1.20
3: Boundary 1.20/1.21
4: Boundary 1.21/1.22
5: Boundary 1.22/1.23
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
1.1b
ENST00000243077
1b
ENSE00001217215
chr12:
57522282-57522814
533
LRP1_HUMAN
1-23
23
0
-
-
1.2
ENST00000243077
2
ENSE00001107512
chr12:
57532242-57532364
123
LRP1_HUMAN
23-64
42
0
-
-
1.3
ENST00000243077
3
ENSE00001107525
chr12:
57535157-57535294
138
LRP1_HUMAN
64-110
47
0
-
-
1.4
ENST00000243077
4
ENSE00000838818
chr12:
57537462-57537581
120
LRP1_HUMAN
110-150
41
0
-
-
1.5
ENST00000243077
5
ENSE00001107561
chr12:
57538755-57538883
129
LRP1_HUMAN
150-193
44
0
-
-
1.6
ENST00000243077
6
ENSE00001107552
chr12:
57539010-57539273
264
LRP1_HUMAN
193-281
89
0
-
-
1.9
ENST00000243077
9
ENSE00001320947
chr12:
57547991-57548153
163
LRP1_HUMAN
281-335
55
0
-
-
1.10
ENST00000243077
10
ENSE00001302177
chr12:
57548262-57548484
223
LRP1_HUMAN
335-409
75
0
-
-
1.11
ENST00000243077
11
ENSE00001330203
chr12:
57549877-57550066
190
LRP1_HUMAN
410-473
64
0
-
-
1.12
ENST00000243077
12
ENSE00001301122
chr12:
57550560-57550703
144
LRP1_HUMAN
473-521
49
0
-
-
1.13
ENST00000243077
13
ENSE00001298063
chr12:
57552185-57552421
237
LRP1_HUMAN
521-600
80
0
-
-
1.14
ENST00000243077
14
ENSE00001299981
chr12:
57553608-57553788
181
LRP1_HUMAN
600-660
61
0
-
-
1.15
ENST00000243077
15
ENSE00001327741
chr12:
57554676-57554898
223
LRP1_HUMAN
660-734
75
0
-
-
1.16
ENST00000243077
16
ENSE00001318771
chr12:
57556100-57556301
202
LRP1_HUMAN
735-802
68
0
-
-
1.17
ENST00000243077
17
ENSE00001295270
chr12:
57556641-57556766
126
LRP1_HUMAN
802-844
43
0
-
-
1.18
ENST00000243077
18
ENSE00001317407
chr12:
57559588-57559728
141
LRP1_HUMAN
844-891
48
0
-
-
1.19
ENST00000243077
19
ENSE00001324415
chr12:
57559867-57559992
126
LRP1_HUMAN
891-933
43
1
B:1-2
2
1.20
ENST00000243077
20
ENSE00001318999
chr12:
57560713-57560829
117
LRP1_HUMAN
933-972
40
1
B:2-41
40
1.21
ENST00000243077
21
ENSE00001290991
chr12:
57561227-57561307
81
LRP1_HUMAN
972-999
28
1
B:41-68
28
1.22
ENST00000243077
22
ENSE00001321501
chr12:
57562923-57563090
168
LRP1_HUMAN
999-1055
57
1
B:68-82
15
1.23
ENST00000243077
23
ENSE00001316630
chr12:
57566951-57567133
183
LRP1_HUMAN
1055-1116
62
0
-
-
1.24
ENST00000243077
24
ENSE00001294437
chr12:
57567563-57567763
201
LRP1_HUMAN
1116-1183
68
0
-
-
1.25
ENST00000243077
25
ENSE00001312663
chr12:
57569243-57569488
246
LRP1_HUMAN
1183-1265
83
0
-
-
1.26
ENST00000243077
26
ENSE00001296112
chr12:
57569692-57569889
198
LRP1_HUMAN
1265-1331
67
0
-
-
1.27
ENST00000243077
27
ENSE00001319703
chr12:
57570824-57571028
205
LRP1_HUMAN
1331-1399
69
0
-
-
1.28
ENST00000243077
28
ENSE00001292073
chr12:
57571210-57571374
165
LRP1_HUMAN
1399-1454
56
0
-
-
1.29
ENST00000243077
29
ENSE00001325523
chr12:
57572142-57572386
245
LRP1_HUMAN
1454-1536
83
0
-
-
1.30
ENST00000243077
30
ENSE00001297961
chr12:
57572673-57572804
132
LRP1_HUMAN
1536-1580
45
0
-
-
1.31
ENST00000243077
31
ENSE00001311178
chr12:
57573112-57573339
228
LRP1_HUMAN
1580-1656
77
0
-
-
1.32
ENST00000243077
32
ENSE00001309278
chr12:
57573565-57573739
175
LRP1_HUMAN
1656-1714
59
0
-
-
1.33
ENST00000243077
33
ENSE00001328727
chr12:
57573830-57573924
95
LRP1_HUMAN
1714-1746
33
0
-
-
1.34
ENST00000243077
34
ENSE00001290948
chr12:
57574113-57574262
150
LRP1_HUMAN
1746-1796
51
0
-
-
1.35
ENST00000243077
35
ENSE00001314212
chr12:
57574450-57574590
141
LRP1_HUMAN
1796-1843
48
0
-
-
1.36
ENST00000243077
36
ENSE00001307564
chr12:
57574940-57575074
135
LRP1_HUMAN
1843-1888
46
0
-
-
1.37
ENST00000243077
37
ENSE00001305812
chr12:
57577162-57577293
132
LRP1_HUMAN
1888-1932
45
0
-
-
1.38
ENST00000243077
38
ENSE00001330334
chr12:
57577558-57577692
135
LRP1_HUMAN
1932-1977
46
0
-
-
1.39
ENST00000243077
39
ENSE00001292593
chr12:
57577868-57577997
130
LRP1_HUMAN
1977-2020
44
0
-
-
1.40
ENST00000243077
40
ENSE00001326661
chr12:
57578109-57578235
127
LRP1_HUMAN
2020-2062
43
0
-
-
1.41
ENST00000243077
41
ENSE00001308210
chr12:
57578622-57578773
152
LRP1_HUMAN
2063-2113
51
0
-
-
1.42
ENST00000243077
42
ENSE00001304021
chr12:
57578864-57578988
125
LRP1_HUMAN
2113-2155
43
0
-
-
1.43
ENST00000243077
43
ENSE00001323007
chr12:
57579314-57579691
378
LRP1_HUMAN
2155-2281
127
0
-
-
1.44
ENST00000243077
44
ENSE00001328642
chr12:
57581050-57581239
190
LRP1_HUMAN
2281-2344
64
0
-
-
1.45
ENST00000243077
45
ENSE00001316690
chr12:
57584588-57584792
205
LRP1_HUMAN
2344-2412
69
0
-
-
1.46
ENST00000243077
46
ENSE00001299409
chr12:
57585103-57585295
193
LRP1_HUMAN
2413-2477
65
0
-
-
1.47
ENST00000243077
47
ENSE00001316808
chr12:
57586628-57586753
126
LRP1_HUMAN
2477-2519
43
0
-
-
1.48
ENST00000243077
48
ENSE00001321088
chr12:
57586959-57587087
129
LRP1_HUMAN
2519-2562
44
0
-
-
1.49
ENST00000243077
49
ENSE00001319306
chr12:
57587349-57587468
120
LRP1_HUMAN
2562-2602
41
0
-
-
1.50
ENST00000243077
50
ENSE00001290843
chr12:
57587682-57587795
114
LRP1_HUMAN
2602-2640
39
0
-
-
1.51
ENST00000243077
51
ENSE00001319434
chr12:
57588137-57588286
150
LRP1_HUMAN
2640-2690
51
0
-
-
1.52
ENST00000243077
52
ENSE00001323838
chr12:
57588360-57588482
123
LRP1_HUMAN
2690-2731
42
0
-
-
1.53
ENST00000243077
53
ENSE00001318058
chr12:
57588768-57588884
117
LRP1_HUMAN
2731-2770
40
0
-
-
1.54
ENST00000243077
54
ENSE00001302141
chr12:
57589054-57589182
129
LRP1_HUMAN
2770-2813
44
0
-
-
1.55
ENST00000243077
55
ENSE00001289847
chr12:
57589441-57589563
123
LRP1_HUMAN
2813-2854
42
0
-
-
1.56
ENST00000243077
56
ENSE00001314255
chr12:
57589646-57589786
141
LRP1_HUMAN
2854-2901
48
0
-
-
1.57
ENST00000243077
57
ENSE00001291411
chr12:
57589870-57590060
191
LRP1_HUMAN
2901-2964
64
0
-
-
1.58
ENST00000243077
58
ENSE00001315700
chr12:
57590765-57590948
184
LRP1_HUMAN
2965-3026
62
0
-
-
1.59
ENST00000243077
59
ENSE00001292871
chr12:
57591082-57591167
86
LRP1_HUMAN
3026-3054
29
0
-
-
1.60
ENST00000243077
60
ENSE00001325742
chr12:
57591328-57591447
120
LRP1_HUMAN
3055-3094
40
0
-
-
1.61
ENST00000243077
61
ENSE00001298595
chr12:
57591939-57592126
188
LRP1_HUMAN
3095-3157
63
0
-
-
1.62
ENST00000243077
62
ENSE00001318488
chr12:
57592248-57592453
206
LRP1_HUMAN
3157-3226
70
0
-
-
1.63
ENST00000243077
63
ENSE00001305366
chr12:
57592995-57593183
189
LRP1_HUMAN
3226-3289
64
0
-
-
1.64
ENST00000243077
64
ENSE00001328542
chr12:
57593660-57593808
149
LRP1_HUMAN
3289-3338
50
0
-
-
1.65
ENST00000243077
65
ENSE00001291635
chr12:
57594225-57594318
94
LRP1_HUMAN
3339-3370
32
0
-
-
1.66
ENST00000243077
66
ENSE00001313605
chr12:
57594482-57594598
117
LRP1_HUMAN
3370-3409
40
0
-
-
1.67
ENST00000243077
67
ENSE00001307582
chr12:
57594817-57594936
120
LRP1_HUMAN
3409-3449
41
0
-
-
1.68
ENST00000243077
68
ENSE00001322267
chr12:
57595280-57595402
123
LRP1_HUMAN
3449-3490
42
0
-
-
1.69
ENST00000243077
69
ENSE00001314694
chr12:
57595563-57595688
126
LRP1_HUMAN
3490-3532
43
0
-
-
1.70
ENST00000243077
70
ENSE00001306379
chr12:
57596204-57596320
117
LRP1_HUMAN
3532-3571
40
0
-
-
1.71
ENST00000243077
71
ENSE00001324059
chr12:
57596964-57597070
107
LRP1_HUMAN
3571-3606
36
0
-
-
1.72
ENST00000243077
72
ENSE00001731153
chr12:
57597172-57597304
133
LRP1_HUMAN
3607-3651
45
0
-
-
1.73
ENST00000243077
73
ENSE00001760982
chr12:
57598193-57598312
120
LRP1_HUMAN
3651-3691
41
0
-
-
1.74
ENST00000243077
74
ENSE00001307523
chr12:
57598410-57598532
123
LRP1_HUMAN
3691-3732
42
0
-
-
1.75
ENST00000243077
75
ENSE00001295680
chr12:
57598892-57599032
141
LRP1_HUMAN
3732-3779
48
0
-
-
1.76
ENST00000243077
76
ENSE00001300743
chr12:
57599134-57599268
135
LRP1_HUMAN
3779-3824
46
0
-
-
1.77
ENST00000243077
77
ENSE00001330472
chr12:
57599341-57599460
120
LRP1_HUMAN
3824-3864
41
0
-
-
1.78
ENST00000243077
78
ENSE00001301800
chr12:
57600256-57600524
269
LRP1_HUMAN
3864-3953
90
0
-
-
1.79
ENST00000243077
79
ENSE00001297467
chr12:
57601821-57601999
179
LRP1_HUMAN
3954-4013
60
0
-
-
1.80
ENST00000243077
80
ENSE00001303363
chr12:
57602494-57602600
107
LRP1_HUMAN
4013-4049
37
0
-
-
1.81
ENST00000243077
81
ENSE00001322130
chr12:
57602866-57602982
117
LRP1_HUMAN
4049-4088
40
0
-
-
1.82
ENST00000243077
82
ENSE00001304178
chr12:
57603475-57603651
177
LRP1_HUMAN
4088-4147
60
0
-
-
1.83
ENST00000243077
83
ENSE00001290032
chr12:
57603812-57603952
141
LRP1_HUMAN
4147-4194
48
0
-
-
1.84
ENST00000243077
84
ENSE00001295389
chr12:
57604090-57604263
174
LRP1_HUMAN
4194-4252
59
0
-
-
1.85
ENST00000243077
85
ENSE00001316267
chr12:
57604501-57604662
162
LRP1_HUMAN
4252-4306
55
0
-
-
1.86
ENST00000243077
86
ENSE00001324584
chr12:
57604959-57605133
175
LRP1_HUMAN
4306-4364
59
0
-
-
1.87
ENST00000243077
87
ENSE00001317091
chr12:
57605270-57605371
102
LRP1_HUMAN
4364-4398
35
0
-
-
1.88
ENST00000243077
88
ENSE00001297966
chr12:
57605533-57605597
65
LRP1_HUMAN
4398-4420
23
0
-
-
1.89
ENST00000243077
89
ENSE00001319205
chr12:
57605710-57605800
91
LRP1_HUMAN
4420-4450
31
0
-
-
1.90
ENST00000243077
90
ENSE00001296038
chr12:
57605900-57606044
145
LRP1_HUMAN
4450-4498
49
0
-
-
1.91
ENST00000243077
91
ENSE00001319616
chr12:
57606198-57607123
926
LRP1_HUMAN
4499-4544
46
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2fyla1 (A:17-97)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
RAP domain-like
(7)
Superfamily
:
RAP domain-like
(7)
Family
:
RAP domain
(7)
Protein domain
:
alpha-2-Macroglobulin receptor associated protein (RAP)
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d2fyla1
A:17-97
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2fylA00 (A:17-97)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Receptor-associated Protein
(5)
Homologous Superfamily
:
Receptor-associated Protein
(5)
Human (Homo sapiens)
(5)
1a
2fylA00
A:17-97
[
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
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 (52 KB)
Header - Asym.Unit
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
2FYL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help