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1IJQ
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE LDL RECEPTOR YWTD-EGF DOMAIN PAIR
Authors
:
H. Jeon, W. Meng, J. Takagi, M. J. Eck, T. A. Springer, S. C. Blacklow
Date
:
27 Apr 01 (Deposition) - 23 May 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Beta-Propeller, Lipid Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Jeon, W. Meng, J. Takagi, M. J. Eck, T. A. Springer, S. C. Blacklow
Implications For Familial Hypercholesterolemia From The Structure Of The Ldl Receptor Ywtd-Egf Domain Pair.
Nat. Struct. Biol. V. 8 499 2001
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Label:
Sorry, no Info available
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SAPs(SNPs)/Variants
(61, 119)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_005376 (A378D, chain A/B, )
02: VAR_005377 (L380H, chain A/B, )
03: VAR_007987 (L380V, chain A/B, )
04: VAR_008995 (F382L, chain A/B, )
05: VAR_072846 (T383P, chain A/B, )
06: VAR_013954 (R385Q, chain A/B, )
07: VAR_072847 (R385W, chain A/B, )
08: VAR_005378 (E387K, chain A/B, )
09: VAR_005379 (L393R, chain A/B, )
10: VAR_062379 (D394G, chain A, )
11: VAR_005380 (R395Q, chain A, )
12: VAR_005381 (R395W, chain A, )
13: VAR_005382 (I402T, chain A/B, )
14: VAR_005383 (V408M, chain A/B, )
15: VAR_005384 (A410T, chain A/B, )
16: VAR_007988 (L411V, chain A/B, )
17: VAR_005385 (D412H, chain A/B, )
18: VAR_005386 (T413K, chain A/B, )
19: VAR_005388 (I420M, chain A/B, )
20: VAR_005387 (I420N, chain A/B, )
21: VAR_072848 (Y421H, chain A/B, )
22: VAR_005389 (W422C, chain A/B, )
23: VAR_062380 (I430T, chain A/B, )
24: VAR_072849 (T433N, chain A/B, )
25: VAR_011863 (V447I, chain A/B, )
26: VAR_065783 (R450G, chain A/B, )
27: VAR_005390 (G457R, chain A/B, )
28: VAR_062381 (L458P, chain A/B, )
29: VAR_005391 (D461H, chain A/B, )
30: VAR_005392 (W462R, chain A/B, )
31: VAR_005394 (H464R, chain A/B, )
32: VAR_072850 (D471N, chain A/B, )
33: VAR_005395 (V502M, chain A/B, )
34: VAR_005396 (P505S, chain A/B, )
35: VAR_005397 (G525D, chain A/B, )
36: VAR_005398 (G528D, chain A/B, )
37: VAR_005399 (N543H, chain A/B, )
38: VAR_005400 (N543S, chain A/B, )
39: VAR_005401 (G544V, chain A/B, )
40: VAR_008996 (L547V, chain A/B, )
41: VAR_072851 (R553C, chain A/B, )
42: VAR_072852 (R553H, chain A/B, )
43: VAR_072853 (W556G, chain A/B, )
44: VAR_072854 (W556S, chain A/B, )
45: VAR_005402 (D558N, chain A/B, )
46: VAR_062382 (D558Y, chain A/B, )
47: VAR_072855 (I564T, chain A/B, )
48: VAR_005403 (G571E, chain A/B, )
49: VAR_072856 (R574W, chain A/B, )
50: VAR_005404 (L578S, chain A/B, )
51: VAR_072857 (D580H, chain A/B, )
52: VAR_007989 (P587S, chain A/B, )
53: VAR_005405 (R612C, chain A/B, )
54: VAR_072858 (V618D, chain A/B, )
55: VAR_005406 (P628L, chain A/B, )
56: VAR_005407 (C646Y, chain A/B, )
57: VAR_005408 (C656R, chain A/B, )
58: VAR_005409 (L661P, chain A/B, )
59: VAR_005410 (P664L, chain A/B, )
60: VAR_013955 (P678L, chain A/B, )
61: VAR_005412 (D679E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_005376
A
399
D
LDLR_HUMAN
Disease (FH)
---
A/B
A
378
D
02
UniProt
VAR_005377
L
401
H
LDLR_HUMAN
Unclassified
---
A/B
L
380
H
03
UniProt
VAR_007987
L
401
V
LDLR_HUMAN
Disease (FH)
---
A/B
L
380
V
04
UniProt
VAR_008995
F
403
L
LDLR_HUMAN
Disease (FH)
---
A/B
F
382
L
05
UniProt
VAR_072846
T
404
P
LDLR_HUMAN
Unclassified
---
A/B
T
383
P
06
UniProt
VAR_013954
R
406
Q
LDLR_HUMAN
Unclassified
---
A/B
R
385
Q
07
UniProt
VAR_072847
R
406
W
LDLR_HUMAN
Unclassified
---
A/B
R
385
W
08
UniProt
VAR_005378
E
408
K
LDLR_HUMAN
Unclassified
---
A/B
E
387
K
09
UniProt
VAR_005379
L
414
R
LDLR_HUMAN
Disease (FH)
---
A/B
L
393
R
10
UniProt
VAR_062379
D
415
G
LDLR_HUMAN
Disease (FH)
---
A
D
394
G
11
UniProt
VAR_005380
R
416
Q
LDLR_HUMAN
Disease (FH)
---
A
R
395
Q
12
UniProt
VAR_005381
R
416
W
LDLR_HUMAN
Disease (FH)
---
A
R
395
W
13
UniProt
VAR_005382
I
423
T
LDLR_HUMAN
Disease (FH)
---
A/B
I
402
T
14
UniProt
VAR_005383
V
429
M
LDLR_HUMAN
Disease (FH)
28942078
A/B
V
408
M
15
UniProt
VAR_005384
A
431
T
LDLR_HUMAN
Unclassified
28942079
A/B
A
410
T
16
UniProt
VAR_007988
L
432
V
LDLR_HUMAN
Disease (FH)
---
A/B
L
411
V
17
UniProt
VAR_005385
D
433
H
LDLR_HUMAN
Disease (FH)
---
A/B
D
412
H
18
UniProt
VAR_005386
T
434
K
LDLR_HUMAN
Unclassified
---
A/B
T
413
K
19
UniProt
VAR_005388
I
441
M
LDLR_HUMAN
Unclassified
---
A/B
I
420
M
20
UniProt
VAR_005387
I
441
N
LDLR_HUMAN
Unclassified
---
A/B
I
420
N
21
UniProt
VAR_072848
Y
442
H
LDLR_HUMAN
Unclassified
---
A/B
Y
421
H
22
UniProt
VAR_005389
W
443
C
LDLR_HUMAN
Unclassified
---
A/B
W
422
C
23
UniProt
VAR_062380
I
451
T
LDLR_HUMAN
Disease (FH)
---
A/B
I
430
T
24
UniProt
VAR_072849
T
454
N
LDLR_HUMAN
Disease (FH)
---
A/B
T
433
N
25
UniProt
VAR_011863
V
468
I
LDLR_HUMAN
Polymorphism
5932
A/B
V
447
I
26
UniProt
VAR_065783
R
471
G
LDLR_HUMAN
Unclassified
---
A/B
R
450
G
27
UniProt
VAR_005390
G
478
R
LDLR_HUMAN
Unclassified
---
A/B
G
457
R
28
UniProt
VAR_062381
L
479
P
LDLR_HUMAN
Disease (FH)
---
A/B
L
458
P
29
UniProt
VAR_005391
D
482
H
LDLR_HUMAN
Disease (FH)
---
A/B
D
461
H
30
UniProt
VAR_005392
W
483
R
LDLR_HUMAN
Disease (FH)
---
A/B
W
462
R
31
UniProt
VAR_005394
H
485
R
LDLR_HUMAN
Unclassified
---
A/B
H
464
R
32
UniProt
VAR_072850
D
492
N
LDLR_HUMAN
Unclassified
---
A/B
D
471
N
33
UniProt
VAR_005395
V
523
M
LDLR_HUMAN
Disease (FH)
28942080
A/B
V
502
M
34
UniProt
VAR_005396
P
526
S
LDLR_HUMAN
Unclassified
---
A/B
P
505
S
35
UniProt
VAR_005397
G
546
D
LDLR_HUMAN
Polymorphism
28942081
A/B
G
525
D
36
UniProt
VAR_005398
G
549
D
LDLR_HUMAN
Disease (FH)
28941776
A/B
G
528
D
37
UniProt
VAR_005399
N
564
H
LDLR_HUMAN
Disease (FH)
28942086
A/B
N
543
H
38
UniProt
VAR_005400
N
564
S
LDLR_HUMAN
Disease (FH)
---
A/B
N
543
S
39
UniProt
VAR_005401
G
565
V
LDLR_HUMAN
Polymorphism
28942082
A/B
G
544
V
40
UniProt
VAR_008996
L
568
V
LDLR_HUMAN
Disease (FH)
---
A/B
L
547
V
41
UniProt
VAR_072851
R
574
C
LDLR_HUMAN
Disease (FH)
---
A/B
R
553
C
42
UniProt
VAR_072852
R
574
H
LDLR_HUMAN
Unclassified
---
A/B
R
553
H
43
UniProt
VAR_072853
W
577
G
LDLR_HUMAN
Disease (FH)
---
A/B
W
556
G
44
UniProt
VAR_072854
W
577
S
LDLR_HUMAN
Unclassified
---
A/B
W
556
S
45
UniProt
VAR_005402
D
579
N
LDLR_HUMAN
Disease (FH)
---
A/B
D
558
N
46
UniProt
VAR_062382
D
579
Y
LDLR_HUMAN
Disease (FH)
---
A/B
D
558
Y
47
UniProt
VAR_072855
I
585
T
LDLR_HUMAN
Unclassified
---
A/B
I
564
T
48
UniProt
VAR_005403
G
592
E
LDLR_HUMAN
Disease (FH)
---
A/B
G
571
E
49
UniProt
VAR_072856
R
595
W
LDLR_HUMAN
Unclassified
---
A/B
R
574
W
50
UniProt
VAR_005404
L
599
S
LDLR_HUMAN
Unclassified
---
A/B
L
578
S
51
UniProt
VAR_072857
D
601
H
LDLR_HUMAN
Unclassified
---
A/B
D
580
H
52
UniProt
VAR_007989
P
608
S
LDLR_HUMAN
Disease (FH)
---
A/B
P
587
S
53
UniProt
VAR_005405
R
633
C
LDLR_HUMAN
Disease (FH)
---
A/B
R
612
C
54
UniProt
VAR_072858
V
639
D
LDLR_HUMAN
Disease (FH)
---
A/B
V
618
D
55
UniProt
VAR_005406
P
649
L
LDLR_HUMAN
Disease (FH)
---
A/B
P
628
L
56
UniProt
VAR_005407
C
667
Y
LDLR_HUMAN
Disease (FH)
28942083
A/B
C
646
Y
57
UniProt
VAR_005408
C
677
R
LDLR_HUMAN
Disease (FH)
---
A/B
C
656
R
58
UniProt
VAR_005409
L
682
P
LDLR_HUMAN
Unclassified
---
A/B
L
661
P
59
UniProt
VAR_005410
P
685
L
LDLR_HUMAN
Disease (FH)
28942084
A/B
P
664
L
60
UniProt
VAR_013955
P
699
L
LDLR_HUMAN
Unclassified
---
A/B
P
678
L
61
UniProt
VAR_005412
D
700
E
LDLR_HUMAN
Disease (FH)
---
A/B
D
679
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 10)
Info
All PROSITE Patterns/Profiles
1: LDLRB (A:418-464,B:418-464|A:465-507,B:46...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LDLRB
PS51120
LDL-receptor class B (LDLRB) repeat profile.
LDLR_HUMAN
439-485
486-528
529-572
573-617
618-658
10
A:418-464
B:418-464
A:465-507
B:465-507
A:508-551
B:508-551
A:552-596
B:552-596
A:597-637
B:597-637
[
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Exons
(0, 0)
Info
All Exons
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ijqa1 (A:377-642)
1b: SCOP_d1ijqb1 (B:377-642)
2a: SCOP_d1ijqa2 (A:643-692)
2b: SCOP_d1ijqb2 (B:643-692)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
YWTD domain
(3)
Family
:
YWTD domain
(3)
Protein domain
:
Low density lipoprotein (LDL) receptor
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1ijqa1
A:377-642
1b
d1ijqb1
B:377-642
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Low density lipoprotein (LDL) receptor, different EGF domains
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1ijqa2
A:643-692
2b
d1ijqb2
B:643-692
[
close SCOP info
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ijqA01 (A:377-638)
1b: CATH_1ijqB01 (B:377-638)
2a: CATH_1ijqA02 (A:639-692)
2b: CATH_1ijqB02 (B:639-692)
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Organisms
(
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(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
Human (Homo sapiens)
(2)
1a
1ijqA01
A:377-638
1b
1ijqB01
B:377-638
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1ijqA02
A:639-692
2b
1ijqB02
B:639-692
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Pfam Domains
(0, 0)
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all PFAM domains
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