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Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (71 KB)
Biol.Unit 2 (141 KB)
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(1)
Title
:
STRUCTURE OF A COMPLEX BETWEEN THE PAIR OF THE LDL RECEPTOR LIGAND-BINDING MODULES 3-4 AND THE RECEPTOR ASSOCIATED PROTEIN (RAP).
Authors
:
N. Beglova, C. Fisher, S. C. Blacklow
Date
:
12 Dec 05 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.26
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Protein-Protein Complex, Rap, Ldlr, Escort Protein, Calcium- Binding, Lipid Transport/Endocytosis/Chaperone Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Fisher, N. Beglova, S. C. Blacklow
Structure Of An Ldlr-Rap Complex Reveals A General Mode For Ligand Recognition By Lipoprotein Receptors
Mol. Cell V. 22 277 2006
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
MPD
5
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NA
4
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE B:105 , ASP B:108 , ASP B:110 , ASP B:112 , ASP B:118 , GLU B:119
BINDING SITE FOR RESIDUE CA B 3001
02
AC2
SOFTWARE
TRP B:144 , ASP B:147 , ASP B:149 , ASP B:151 , ASP B:157 , GLU B:158
BINDING SITE FOR RESIDUE CA B 3002
03
AC3
SOFTWARE
HOH A:61 , HOH A:73 , GLU A:265 , GLU A:269 , HOH B:5023
BINDING SITE FOR RESIDUE NA A 5001
04
AC4
SOFTWARE
LYS B:86 , GLY B:98 , HOH B:5003 , HOH B:5004 , HOH B:5012
BINDING SITE FOR RESIDUE NA B 5002
05
AC5
SOFTWARE
HOH A:68 , HOH A:110 , ASP A:228 , SER A:232
BINDING SITE FOR RESIDUE NA A 5003
06
AC6
SOFTWARE
HOH A:56 , HOH A:91 , HOH A:121 , LEU A:240 , HOH B:5014
BINDING SITE FOR RESIDUE NA A 5004
07
AC7
SOFTWARE
HIS A:259 , ASP B:151 , GLU B:153
BINDING SITE FOR RESIDUE MPD A 4001
08
AC8
SOFTWARE
HOH A:145 , GLU A:217 , PHE A:218 , ARG A:244 , LYS A:248 , LYS A:298
BINDING SITE FOR RESIDUE MPD A 4002
09
AC9
SOFTWARE
GLN B:133
BINDING SITE FOR RESIDUE MPD B 4003
10
BC1
SOFTWARE
PRO B:129 , ASN B:135 , SER B:137 , GLN B:142
BINDING SITE FOR RESIDUE MPD B 4004
11
BC2
SOFTWARE
ARG A:222 , GLY A:313 , SER A:316 , THR B:87 , CYS B:88 , SER B:89 , GLN B:90
BINDING SITE FOR RESIDUE MPD B 4005
[
close Site info
]
SAPs(SNPs)/Variants
(25, 25)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_005316 (C88R, chain B, )
02: VAR_005317 (C95R, chain B, )
03: VAR_062371 (C113F, chain B, )
04: VAR_062372 (C113W, chain B, )
05: VAR_065780 (D118H, chain B, )
06: VAR_005318 (E119K, chain B, )
07: VAR_072828 (C122R, chain B, )
08: VAR_072829 (C127Y, chain B, )
09: VAR_005319 (C134G, chain B, )
10: VAR_072830 (C134Y, chain B, )
11: VAR_005320 (C139Y, chain B, )
12: VAR_072831 (D147A, chain B, )
13: VAR_005321 (D147H, chain B, )
14: VAR_005322 (D147N, chain B, )
15: VAR_005323 (D147Y, chain B, )
16: VAR_013950 (D151H, chain B, )
17: VAR_072832 (D151N, chain B, )
18: VAR_005324 (C152R, chain B, )
19: VAR_005325 (C152W, chain B, )
20: VAR_005326 (D154N, chain B, )
21: VAR_007981 (D154Y, chain B, )
22: VAR_005327 (S156L, chain B, )
23: VAR_072833 (C163W, chain B, )
24: VAR_013951 (C163Y, chain B, )
25: VAR_011821 (V277M, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_005316
C
109
R
LDLR_HUMAN
Unclassified
---
B
C
88
R
02
UniProt
VAR_005317
C
116
R
LDLR_HUMAN
Disease (FH)
---
B
C
95
R
03
UniProt
VAR_062371
C
134
F
LDLR_HUMAN
Disease (FH)
---
B
C
113
F
04
UniProt
VAR_062372
C
134
W
LDLR_HUMAN
Disease (FH)
---
B
C
113
W
05
UniProt
VAR_065780
D
139
H
LDLR_HUMAN
Unclassified
---
B
D
118
H
06
UniProt
VAR_005318
E
140
K
LDLR_HUMAN
Disease (FH)
---
B
E
119
K
07
UniProt
VAR_072828
C
143
R
LDLR_HUMAN
Disease (FH)
---
B
C
122
R
08
UniProt
VAR_072829
C
148
Y
LDLR_HUMAN
Disease (FH)
---
B
C
127
Y
09
UniProt
VAR_005319
C
155
G
LDLR_HUMAN
Unclassified
---
B
C
134
G
10
UniProt
VAR_072830
C
155
Y
LDLR_HUMAN
Disease (FH)
---
B
C
134
Y
11
UniProt
VAR_005320
C
160
Y
LDLR_HUMAN
Unclassified
---
B
C
139
Y
12
UniProt
VAR_072831
D
168
A
LDLR_HUMAN
Unclassified
---
B
D
147
A
13
UniProt
VAR_005321
D
168
H
LDLR_HUMAN
Disease (FH)
---
B
D
147
H
14
UniProt
VAR_005322
D
168
N
LDLR_HUMAN
Disease (FH)
---
B
D
147
N
15
UniProt
VAR_005323
D
168
Y
LDLR_HUMAN
Disease (FH)
---
B
D
147
Y
16
UniProt
VAR_013950
D
172
H
LDLR_HUMAN
Unclassified
---
B
D
151
H
17
UniProt
VAR_072832
D
172
N
LDLR_HUMAN
Disease (FH)
---
B
D
151
N
18
UniProt
VAR_005324
C
173
R
LDLR_HUMAN
Unclassified
---
B
C
152
R
19
UniProt
VAR_005325
C
173
W
LDLR_HUMAN
Disease (FH)
---
B
C
152
W
20
UniProt
VAR_005326
D
175
N
LDLR_HUMAN
Disease (FH)
---
B
D
154
N
21
UniProt
VAR_007981
D
175
Y
LDLR_HUMAN
Disease (FH)
---
B
D
154
Y
22
UniProt
VAR_005327
S
177
L
LDLR_HUMAN
Disease (FH)
---
B
S
156
L
23
UniProt
VAR_072833
C
184
W
LDLR_HUMAN
Disease (FH)
---
B
C
163
W
24
UniProt
VAR_013951
C
184
Y
LDLR_HUMAN
Disease (FH)
---
B
C
163
Y
25
UniProt
VAR_011821
V
311
M
AMRP_HUMAN
Polymorphism
1800493
A
V
277
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: LDLRA_2 (-|-|B:87-123|B:126-163|-|-|-)
2: LDLRA_1 (-|-|B:100-122|B:139-163|-|-|-)
3: ER_TARGET (A:320-320)
;
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.
LDLR_HUMAN
26-64
67-105
108-144
147-185
196-232
235-271
275-314
2
-
-
B:87-123
B:126-163
-
-
-
2
LDLRA_1
PS01209
LDL-receptor class A (LDLRA) domain signature.
LDLR_HUMAN
39-63
82-104
121-143
160-184
209-231
248-270
289-313
2
-
-
B:100-122
B:139-163
-
-
-
3
ER_TARGET
PS00014
Endoplasmic reticulum targeting sequence.
AMRP_HUMAN
354-357
1
A:320-320
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d2fcwa1 (A:216-320)
2a: SCOP_d2fcwb1 (B:86-124)
2b: SCOP_d2fcwb2 (B:125-163)
View:
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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
d2fcwa1
A:216-320
Class
:
Small proteins
(3458)
Fold
:
LDL receptor-like module
(20)
Superfamily
:
LDL receptor-like module
(20)
Family
:
LDL receptor-like module
(19)
Protein domain
:
Ligand-binding domain of low-density lipoprotein receptor
(13)
Human (Homo sapiens) [TaxId: 9606]
(13)
2a
d2fcwb1
B:86-124
2b
d2fcwb2
B:125-163
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2fcwB02 (B:122-163)
1b: CATH_2fcwB01 (B:86-121)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Low-density Lipoprotein Receptor
(15)
Homologous Superfamily
:
Low-density Lipoprotein Receptor
(15)
Human (Homo sapiens)
(12)
1a
2fcwB02
B:122-163
1b
2fcwB01
B:86-121
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
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Nucleic
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Sidechain
Hetero
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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