3CKP - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

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 :   2.30

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
PubMed-ID: 18434152 | Reference-DOI: 10.1016/J.BMCL.2008.03.081
(for further references see the PDB file header)

Molecule 1 - BETA-SECRETASE 1
	Chains	:	A, B, C
	EC Number	:	3.4.23.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Fragment	:	PROTEASE DOMAIN, UNP RESIDUES 43-454
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, MEMBRANE- ASSOCIATED ASPARTIC PROTEASE 2, MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	012	3	Ligand/Ion	(4S)-N-[(1S,2R)-1-BENZYL-3-{[3-(DIMETHYLAMINO)BENZYL]AMINO}-2-HYDROXYPROPYL]-1-(3-METHOXYBENZYL)-2-OXOIMIDAZOLIDINE-4-CARBOXAMIDE
2	CL	9	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	012	1	Ligand/Ion	(4S)-N-[(1S,2R)-1-BENZYL-3-{[3-(DIMETHYLAMINO)BENZYL]AMINO}-2-HYDROXYPROPYL]-1-(3-METHOXYBENZYL)-2-OXOIMIDAZOLIDINE-4-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	012	1	Ligand/Ion	(4S)-N-[(1S,2R)-1-BENZYL-3-{[3-(DIMETHYLAMINO)BENZYL]AMINO}-2-HYDROXYPROPYL]-1-(3-METHOXYBENZYL)-2-OXOIMIDAZOLIDINE-4-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	012	1	Ligand/Ion	(4S)-N-[(1S,2R)-1-BENZYL-3-{[3-(DIMETHYLAMINO)BENZYL]AMINO}-2-HYDROXYPROPYL]-1-(3-METHOXYBENZYL)-2-OXOIMIDAZOLIDINE-4-CARBOXAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU C:1 , MET C:2	BINDING SITE FOR RESIDUE CL C 604
2	AC2	SOFTWARE	LYS A:75 , GLU A:77	BINDING SITE FOR RESIDUE CL A 607
3	AC3	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 , PHE A:108 , ILE A:110 , ARG A:128 , TYR A:198 , ASP A:228 , SER A:229 , GLY A:230 , THR A:231 , THR A:232 , HOH A:679	BINDING SITE FOR RESIDUE 012 A 501
4	AC4	SOFTWARE	GLN B:12 , GLY B:13 , ASP B:32 , GLY B:34 , PRO B:70 , TYR B:71 , THR B:72 , PHE B:108 , TRP B:115 , ASP B:228 , GLY B:230 , THR B:231 , THR B:232 , HOH B:613	BINDING SITE FOR RESIDUE 012 B 502
5	AC5	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 , PHE C:108 , ILE C:110 , TYR C:198 , SER C:229 , GLY C:230 , THR C:231 , THR C:232	BINDING SITE FOR RESIDUE 012 C 503

Asymmetric Unit

No.	Residues
1	A:155	-	A:359
2	A:217	-	A:382
3	A:269	-	A:319
4	B:155	-	B:359
5	B:217	-	B:382
6	B:269	-	B:319
7	C:155	-	C:359
8	C:217	-	C:382
9	C:269	-	C:319

Asymmetric Unit

No.	Residues
1	Ser A:22	-	Pro A:23
2	Arg A:128	-	Pro A:129
3	Gly A:372	-	Pro A:373
4	Ser B:22	-	Pro B:23
5	Arg B:128	-	Pro B:129
6	Gly B:372	-	Pro B:373
7	Ser C:22	-	Pro C:23
8	Arg C:128	-	Pro C:129
9	Gly C:372	-	Pro C:373

Asymmetric Unit (1, 3)

								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)

Biological Unit 1 (1, 1)

								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	V	204	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								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)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_060692	V	265	A	BACE1_HUMAN	Polymorphism	28989503	C	V	204	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 6)

	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

Biological Unit 1 (2, 2)

	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	A:14-355 - -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	BACE1_HUMAN	90-101	1	A:29-40 - -

Biological Unit 2 (2, 2)

	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 -

Biological Unit 3 (2, 2)

	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	- - C:14-355
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	BACE1_HUMAN	90-101	1	- - C:29-40

Asymmetric Unit (9, 27)

	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

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:379
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:392
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445  
          BACE1_HUMAN    56 RRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 447
               SCOP domains d3ckpa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------3ckpA01 A:14-146 Acid Proteases                                                                                                      3ckpA02 A:14         7-386 Acid Proteases                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee...---------.eeeeeeee...hhh.eeeeeeeee..........eeeeee..ee.....hhhhh..eee......eeeehhhhhhhhhhhhhhh...............eeee....hhhhh..eeeeee.....eeeeeeehhhhheee..----..eeeeee...ee...eeehhhhhh.eeeeee....eeeeeee...........eeeeeee...hhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------PEPTIDASE_A1  PDB: A:14-355 UniProt: 75-416                                                                                                                                                                                                                                                                                                           ------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: A:-6-26         Exon 1.2d  PDB: A:27-56       ------------------------------------------------------------------------Exon 1.5b  PDB: A:129-174 (gaps)              Exon 1.6b  PDB: A:175-219 UniProt: 236-280   Exon 1.7c  PDB: A:220-253         Exon 1.8b  PDB: A:254-303 UniProt: 315-364        ---------------------------------------------------------Exon 1.10f  PDB: A:361-386 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.4c  PDB: A:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: A:304-361 (gaps) UniProt: 365-422         ------------------------- Transcript 1 (2)
                 3ckp A  -6 KKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAG---------ASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE----SQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 386
                                 ||  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154   |     -   |   174       184       194       204       214       224       234       244       254       264       274       284       294       304     |   -|      324       334       344       354       364       374       384  
                                -1|                                                                                                                                                          158       168                                                                                                                                           310  315                                                                       
                                  1

Chain B from PDB  Type:PROTEIN  Length:376
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:388
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439        
          BACE1_HUMAN    60 FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 447
               SCOP domains d3ckpb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------3ckpB01 B:14-146 Acid Proteases                                                                                                      3ckpB02 B:            147-386 Acid Proteases                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhh......eeeeee.------------.eeeeeee...hhh.eeeeeeeee.......ee.eeeeee..ee...hhhhh....eee......eeehhhhhhhhhhhhhhhh...............eeee....hhhhh..eeeeee.....eeeeeeehhhhheee........eeeeee.eee....eeehhhhhh.eeeeee....eeeeeee...........eeeeeee..hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: B:14-355 UniProt: 75-416                                                                                                                                                                                                                                                                                                           ------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: B:-2-26     Exon 1.2d  PDB: B:27-56       ------------------------------------------------------------------------Exon 1.5b  PDB: B:129-174 (gaps)              Exon 1.6b  PDB: B:175-219 UniProt: 236-280   Exon 1.7c  PDB: B:220-253         Exon 1.8b  PDB: B:254-303 UniProt: 315-364        ---------------------------------------------------------Exon 1.10f  PDB: B:361-386 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.4c  PDB: B:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: B:304-361 UniProt: 365-422                ------------------------- Transcript 1 (2)
                 3ckp B  -2 FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCG------------SVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 386
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       | -         -|      178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378        
                            -1|                                                                                                                                                        156          169                                                                                                                                                                                                                         
                              1

Chain C from PDB  Type:PROTEIN  Length:377
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:391
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446 
          BACE1_HUMAN    57 RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 447
               SCOP domains d3ckpc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------3ckpC01 C:14-146 Acid Proteases                                                                                                      3ckpC02 C:            147-386 Acid Proteases                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeeee..eeeeeeeee.eee.......eee..eeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee.------------..eeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh.......hhhhh...eeee....hhhhh..eeeeee.....eeeeeeehhhhheeee.--....eeeeee.eeee...eeehhhhhh..eeeeehhh.eeeeeee...........eeeeeee...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------PEPTIDASE_A1  PDB: C:14-355 UniProt: 75-416                                                                                                                                                                                                                                                                                                           ------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: C:-5-26        Exon 1.2d  PDB: C:27-56       ------------------------------------------------------------------------Exon 1.5b  PDB: C:129-174 (gaps)              Exon 1.6b  PDB: C:175-219 UniProt: 236-280   Exon 1.7c  PDB: C:220-253         Exon 1.8b  PDB: C:254-303 UniProt: 315-364        ---------------------------------------------------------Exon 1.10f  PDB: C:361-386 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4c  PDB: C:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: C:304-361 (gaps) UniProt: 365-422         ------------------------- Transcript 1 (2)
                 3ckp C  -5 KGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCG------------SVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE--ATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI 386
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155|        -   |   175       185       195       205       215       225       235       245       255       265       275       285       295       305    |  315       325       335       345       355       365       375       385 
                               -1|                                                                                                                                                        156          169                                                                                                                                          310  |                                                                         
                                 1                                                                                                                                                                                                                                                                                                                     313

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

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	d3ckpa_	A:
1b	d3ckpb_	B:
1c	d3ckpc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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	3ckpA01	A:14-146
1b	3ckpB01	B:14-146
1c	3ckpC01	C:14-146
1d	3ckpC02	C:147-386
1e	3ckpA02	A:147-386
1f	3ckpB02	B:147-386

(no "Pfam Domain" information available for 3CKP)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (BACE1_HUMAN | P56817)

molecular function
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0008798	beta-aspartyl-peptidase activity	Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0050435	amyloid-beta metabolic process	The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0006509	membrane protein ectodomain proteolysis	The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0070931	Golgi-associated vesicle lumen	The volume enclosed by the membrane of a Golgi-associated vesicle.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005802	trans-Golgi network	The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:128 - Pro A:129	[ RasMol ]
		Arg B:128 - Pro B:129	[ RasMol ]
		Arg C:128 - Pro C:129	[ RasMol ]
		Gly A:372 - Pro A:373	[ RasMol ]
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		Gly C:372 - Pro C:373	[ RasMol ]
		Ser A:22 - Pro A:23	[ RasMol ]
		Ser B:22 - Pro B:23	[ RasMol ]
		Ser C:22 - Pro C:23	[ RasMol ]

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	3ckp
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	BACE1_HUMAN \| P56817
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	3.4.23.46
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (5, 5)

SS Bonds (9, 9)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

PROSITE Motifs (2, 6)

Exons (9, 27)

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SCOP Domains (1, 3)

CATH Domains (1, 6)

Pfam Domains (0, 0)

Gene Ontology (30, 30)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File