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Biol. Unit 1
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
(1, 5)
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
-1
Ligand/Ion
CALCIUM ION
2
MPD
5
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NA
-1
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 only available for the asymmetric unit)
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 ()
2: LDLRA_1 ()
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.
(no "Exon" information available for biological units yet)
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:
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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
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain B
Asymmetric Unit 1
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