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3MSJ
Biol. Unit 2
Info
Asym.Unit (389 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (135 KB)
Biol.Unit 3 (128 KB)
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(1)
Title
:
STRUCTURE OF BACE (BETA SECRETASE) IN COMPLEX WITH INHIBITOR
Authors
:
J. Madden, J. Kramer, M. A. Smith, J. Barker, R. Godemann
Date
:
29 Apr 10 (Deposition) - 14 Jul 10 (Release) - 25 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Protease, Alzheimer'S Disease, Aspartic Protease, Aspartyl Protease, Base, Beta-Secretase, Glycoprotein, Hydrolase, Memapsin 2, Amyloid Precursor Protein Secretases, Aspartic Endopeptidases, Fragment- Based Drug Design, Fluorescence Polarisation, Transmembrane, Zymogen, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. Madden, J. R. Dod, R. Godemann, J. Kraemer, M. Smith, M. Biniszkiewicz, D. J. Hallett, J. Barker, J. D. Dyekjaer, T. Hesterkamp
Fragment-Based Discovery And Optimization Of Bace1 Inhibitors.
Bioorg. Med. Chem. Lett. V. 20 5329 2010
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: 3-(2-AMINO-5-CHLORO-1H-BENZIMIDAZO... (EV3a)
1b: 3-(2-AMINO-5-CHLORO-1H-BENZIMIDAZO... (EV3b)
1c: 3-(2-AMINO-5-CHLORO-1H-BENZIMIDAZO... (EV3c)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
View:
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Label:
No.
Name
Count
Type
Full Name
1
EV3
1
Ligand/Ion
3-(2-AMINO-5-CHLORO-1H-BENZIMIDAZOL-1-YL)PROPAN-1-OL
2
GOL
8
Ligand/Ion
GLYCEROL
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Sites
(9, 9)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
8: BC7 (SOFTWARE)
9: BC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
ASP B:32 , GLY B:34 , TYR B:71 , TRP B:76 , ILE B:226 , ASP B:228 , GOL B:401
BINDING SITE FOR RESIDUE EV3 B 393
2
BC1
SOFTWARE
ASN A:98 , SER A:132 , GLU A:134 , PHE B:-1 , SER B:-2 , VAL B:0 , GLU B:1 , HOH B:536 , HOH B:613
BINDING SITE FOR RESIDUE GOL B 394
3
BC2
SOFTWARE
SER B:86 , ILE B:87 , PRO B:88 , ASN B:92 , VAL B:93 , THR B:94 , HOH B:446 , HOH B:640
BINDING SITE FOR RESIDUE GOL B 395
4
BC3
SOFTWARE
VAL B:3 , ASP B:4 , ASN B:5 , HIS B:89
BINDING SITE FOR RESIDUE GOL B 396
5
BC4
SOFTWARE
LYS B:9 , GLY B:11 , GLY B:13 , VAL B:170 , THR B:232 , GLU B:339
BINDING SITE FOR RESIDUE GOL B 397
6
BC5
SOFTWARE
THR B:19 , VAL B:20 , GLY B:21 , SER B:22 , PRO B:24 , LEU B:84 , SER B:86 , THR B:94
BINDING SITE FOR RESIDUE GOL B 398
7
BC6
SOFTWARE
GLU B:77 , GLU B:104 , SER B:105 , HOH B:544 , ASP C:131
BINDING SITE FOR RESIDUE GOL B 399
8
BC7
SOFTWARE
VAL B:204 , ARG B:205 , VAL B:206 , ASP B:212 , LYS B:214 , MET B:215 , TYR B:220 , HOH B:552 , HOH B:600
BINDING SITE FOR RESIDUE GOL B 400
9
BC8
SOFTWARE
LEU B:30 , PHE B:108 , EV3 B:393
BINDING SITE FOR RESIDUE GOL B 401
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_060692 (V204A, chain B, )
View:
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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
B
V
204
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PEPTIDASE_A1 (B:14-355)
2: ASP_PROTEASE (B: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
1
-
B:14-355
-
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
BACE1_HUMAN
90-101
1
-
B:29-40
-
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3msja_ (A:)
1b: SCOP_d3msjb_ (B:)
1c: SCOP_d3msjc_ (C:)
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Protein Domains
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Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Pepsin-like
(505)
Protein domain
:
beta-secretase (memapsin)
(237)
Human (Homo sapiens) [TaxId: 9606]
(237)
1a
d3msja_
A:
1b
d3msjb_
B:
1c
d3msjc_
C:
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Asp_3msjC01 (C:13-357)
1b: PFAM_Asp_3msjC02 (C:13-357)
1c: PFAM_Asp_3msjC03 (C:13-357)
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Clan
:
Peptidase_AA
(368)
Family
:
Asp
(155)
Homo sapiens (Human)
(116)
1a
Asp-3msjC01
C:13-357
1b
Asp-3msjC02
C:13-357
1c
Asp-3msjC03
C:13-357
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Chain B
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (389 KB)
Header - Asym.Unit
Biol.Unit 1 (129 KB)
Header - Biol.Unit 1
Biol.Unit 2 (135 KB)
Header - Biol.Unit 2
Biol.Unit 3 (128 KB)
Header - Biol.Unit 3
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