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3CKR
Asym. Unit
Info
Asym.Unit (194 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (66 KB)
Biol.Unit 3 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH INHIBITOR
Authors
:
K. Min
Date
:
16 Mar 08 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Beta-Secretase, Aspartyl Protease, Alternative Splicing, Glycoprotein, Hydrolase, Membrane, Transmembrane, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Park, K. Min, H. -S. Kwak, K. D. Koo, D. Lim, S. -W. Seo, J. -U. Choi, B. Platt, D. -Y. Choi
Synthesis, Sar, And X-Ray Structure Of Human Bace-1 Inhibitors With Cyclic Urea Derivatives
Bioorg. Med. Chem. Lett. V. 18 2900 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 3)
Info
All Hetero Components
1a: (4S)-1,4-DIBENZYL-N-[(1S,2R)-1-BEN... (009a)
1b: (4S)-1,4-DIBENZYL-N-[(1S,2R)-1-BEN... (009b)
1c: (4S)-1,4-DIBENZYL-N-[(1S,2R)-1-BEN... (009c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
009
3
Ligand/Ion
(4S)-1,4-DIBENZYL-N-[(1S,2R)-1-BENZYL-3-{[3-(DIMETHYLAMINO)BENZYL]AMINO}-2-HYDROXYPROPYL]-2-OXOIMIDAZOLIDINE-4-CARBOXAMIDE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:12 , GLY A:13 , ASP A:32 , GLY A:34 , SER A:35 , PRO A:70 , TYR A:71 , THR A:72 , GLN A:73 , PHE A:108 , ILE A:110 , ARG A:128 , TYR A:198 , ASP A:228 , GLY A:230 , THR A:231 , THR A:232
BINDING SITE FOR RESIDUE 009 A 501
2
AC2
SOFTWARE
GLY B:11 , GLN B:12 , GLY B:13 , ASP B:32 , GLY B:34 , TYR B:71 , THR B:72 , GLN B:73 , PHE B:108 , ILE B:110 , ILE B:126 , GLY B:230 , THR B:231 , THR B:232 , ARG B:235
BINDING SITE FOR RESIDUE 009 B 502
3
AC3
SOFTWARE
GLY C:11 , GLN C:12 , GLY C:13 , LEU C:30 , ASP C:32 , GLY C:34 , PRO C:70 , TYR C:71 , THR C:72 , GLN C:73 , PHE C:108 , ILE C:110 , TYR C:198 , GLY C:230 , THR C:231 , THR C:232
BINDING SITE FOR RESIDUE 009 C 503
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SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_060692 (V204A, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_060692
V
265
A
BACE1_HUMAN
Polymorphism
28989503
A/B/C
V
204
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PEPTIDASE_A1 (A:14-355,B:14-355,C:14-355)
2: ASP_PROTEASE (A:29-40,B:29-40,C:29-40)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPTIDASE_A1
PS51767
Peptidase family A1 domain profile.
BACE1_HUMAN
75-416
3
A:14-355
B:14-355
C:14-355
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
BACE1_HUMAN
90-101
3
A:29-40
B:29-40
C:29-40
[
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Exons
(9, 27)
Info
All Exons
Exon 1.1b (A:-6-26 | B:-2-26 | C:-5-26)
Exon 1.2d (A:27-56 | B:27-56 | C:27-56)
Exon 1.4c (A:56-128 | B:56-128 | C:56-128)
Exon 1.5b (A:129-174 (gaps) | B:129-174 (gaps...)
Exon 1.6b (A:175-219 | B:175-219 | C:175-219)
Exon 1.7c (A:220-253 | B:220-253 | C:220-253)
Exon 1.8b (A:254-303 | B:254-303 | C:254-303)
Exon 1.9d (A:304-361 (gaps) | B:304-361 | C:3...)
Exon 1.10f (A:361-386 | B:361-386 | C:361-386)
View:
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All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2d
03: Boundary 1.2d/1.4c
04: Boundary 1.4c/1.5b
05: Boundary 1.5b/1.6b
06: Boundary 1.6b/1.7c
07: Boundary 1.7c/1.8b
08: Boundary 1.8b/1.9d
09: Boundary 1.9d/1.10f
10: Boundary 1.10f/-
View:
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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
ENST00000313005
1b
ENSE00002169377
chr11:
117186972-117186251
722
BACE1_HUMAN
1-87
87
3
A:-6-26
B:-2-26
C:-5-26
32
28
31
1.2d
ENST00000313005
2d
ENSE00001779698
chr11:
117167677-117167589
89
BACE1_HUMAN
88-117
30
3
A:27-56
B:27-56
C:27-56
30
30
30
1.4c
ENST00000313005
4c
ENSE00001602221
chr11:
117166063-117165847
217
BACE1_HUMAN
117-189
73
3
A:56-128
B:56-128
C:56-128
73
73
73
1.5b
ENST00000313005
5b
ENSE00001732292
chr11:
117164724-117164587
138
BACE1_HUMAN
190-235
46
3
A:129-174 (gaps)
B:129-174 (gaps)
C:129-174 (gaps)
46
46
46
1.6b
ENST00000313005
6b
ENSE00001231658
chr11:
117163904-117163770
135
BACE1_HUMAN
236-280
45
3
A:175-219
B:175-219
C:175-219
45
45
45
1.7c
ENST00000313005
7c
ENSE00001053358
chr11:
117162529-117162428
102
BACE1_HUMAN
281-314
34
3
A:220-253
B:220-253
C:220-253
34
34
34
1.8b
ENST00000313005
8b
ENSE00001053366
chr11:
117161765-117161616
150
BACE1_HUMAN
315-364
50
3
A:254-303
B:254-303
C:254-303
50
50
50
1.9d
ENST00000313005
9d
ENSE00001385289
chr11:
117161375-117161204
172
BACE1_HUMAN
365-422
58
3
A:304-361 (gaps)
B:304-361
C:304-361 (gaps)
58
58
58
1.10f
ENST00000313005
10f
ENSE00002041784
chr11:
117160523-117156402
4122
BACE1_HUMAN
422-501
80
3
A:361-386
B:361-386
C:361-386
26
26
26
[
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3ckra_ (A:)
1b: SCOP_d3ckrb_ (B:)
1c: SCOP_d3ckrc_ (C:)
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(
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Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Pepsin-like
(505)
Protein domain
:
automated matches
(64)
Human (Homo sapiens) [TaxId: 9606]
(38)
1a
d3ckra_
A:
1b
d3ckrb_
B:
1c
d3ckrc_
C:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3ckrA01 (A:14-146)
1b: CATH_3ckrB01 (B:14-146)
1c: CATH_3ckrC01 (C:14-146)
1d: CATH_3ckrC02 (C:147-386)
1e: CATH_3ckrA02 (A:147-386)
1f: CATH_3ckrB02 (B:147-386)
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Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
Human (Homo sapiens)
(161)
1a
3ckrA01
A:14-146
1b
3ckrB01
B:14-146
1c
3ckrC01
C:14-146
1d
3ckrC02
C:147-386
1e
3ckrA02
A:147-386
1f
3ckrB02
B:147-386
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (194 KB)
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