1YM2 - JenaLib

Asym.Unit - manually (Jmol Viewer)

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 HUMAN BETA SECRETASE COMPLEXED WITH NVP-AUR200

Authors :   S. Hanessian, H. Yun, Y. Hou, G. Yang, M. Bayrakdarian, E. Therrien, N. Moitessier, S. Roggo, S. Veenstra

Date :   20 Jan 05 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,X,Y,Z
Biol. Unit 1: A,X  (1x)
Biol. Unit 2: B,Y  (1x)
Biol. Unit 3: C,Z  (1x)

Keywords :   Beta-Secretase, Memapsin2, Alzheimer'S Disease, Aspartic Protease, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hanessian, H. Yun, Y. Hou, G. Yang, M. Bayrakdarian, E. Therrien, N. Moitessier, S. Roggo, S. Veenstra, M. Tintelnot-Blomley, J. M. Rondeau, C. Ostermeier, A. Strauss, P. Ramage, P. Paganetti, U. Neumann, C. Betschart
Structure-Based Design, Synthesis, And Memapsin 2 (Bace) Inhibitory Activity Of Carbocyclic And Heterocyclic Peptidomimetics
J. Med. Chem. V. 48 5175 2005
PubMed-ID: 16078837 | Reference-DOI: 10.1021/JM050142+

Molecule 1 - BETA-SECRETASE 1
	Chains	:	A, B, C
	EC Number	:	3.4.23.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 48-447
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 1, ASPARTYL PROTEASE 2, ASP 2, ASP2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, MEMAPSIN-2

Molecule 2 - NVP-AUR200 INHIBITOR
	Chains	:	X, Y, Z
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	X	Y	Z
Biological Unit 1 (1x)	:	A			X
Biological Unit 2 (1x)	:		B			Y
Biological Unit 3 (1x)	:			C			Z

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	24O	3	Mod. Amino Acid	(1R,2R)-2-[(1S,2S)-2-AMINO-1-HYDROXY-4-METHYLPENTYL]-4-OXOCYCLOPENTANECARBOXYLIC ACID
2	ACE	3	Mod. Amino Acid	ACETYL GROUP
3	LYT	3	Mod. Amino Acid	BUTYLAMINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	24O	1	Mod. Amino Acid	(1R,2R)-2-[(1S,2S)-2-AMINO-1-HYDROXY-4-METHYLPENTYL]-4-OXOCYCLOPENTANECARBOXYLIC ACID
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	LYT	1	Mod. Amino Acid	BUTYLAMINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	24O	1	Mod. Amino Acid	(1R,2R)-2-[(1S,2S)-2-AMINO-1-HYDROXY-4-METHYLPENTYL]-4-OXOCYCLOPENTANECARBOXYLIC ACID
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	LYT	1	Mod. Amino Acid	BUTYLAMINE

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	24O	1	Mod. Amino Acid	(1R,2R)-2-[(1S,2S)-2-AMINO-1-HYDROXY-4-METHYLPENTYL]-4-OXOCYCLOPENTANECARBOXYLIC ACID
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	LYT	1	Mod. Amino Acid	BUTYLAMINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:30 , ASP A:32 , GLY A:34 , VAL A:69 , PRO A:70 , TYR A:71 , THR A:72 , GLN A:73 , ILE A:110 , ILE A:126 , TYR A:198 , ASP A:228 , GLY A:230 , THR A:231 , THR A:232 , ARG A:235 , HOH A:1026 , HOH A:1040 , HOH A:1177 , HOH X:1016 , HOH X:1017 , HOH X:1196	BINDING SITE FOR CHAIN X OF NVP-AUR200 INHIBITOR
2	AC2	SOFTWARE	GLY B:11 , GLN B:12 , GLY B:13 , LEU B:30 , ASP B:32 , GLY B:34 , PRO B:70 , TYR B:71 , THR B:72 , GLN B:73 , ILE B:110 , ILE B:126 , TYR B:198 , ASP B:228 , GLY B:230 , THR B:231 , THR B:232 , ARG B:235 , HOH B:2026 , HOH B:2030 , HOH Y:2010 , HOH Y:2029 , HOH Y:2058	BINDING SITE FOR CHAIN Y OF NVP-AUR200 INHIBITOR
3	AC3	SOFTWARE	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 , ILE C:110 , ILE C:126 , TYR C:198 , ASP C:228 , GLY C:230 , THR C:231 , THR C:232 , ARG C:235 , HOH C:3035 , HOH C:3041 , HOH Z:3020 , HOH Z:3043 , HOH Z:3090	BINDING SITE FOR CHAIN Z OF NVP-AUR200 INHIBITOR

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	Tyr A:222	-	Asp A:223
4	Gly A:372	-	Pro A:373
5	Ser B:22	-	Pro B:23
6	Arg B:128	-	Pro B:129
7	Tyr B:222	-	Asp B:223
8	Gly B:372	-	Pro B:373
9	Ser C:22	-	Pro C:23
10	Arg C:128	-	Pro C:129
11	Tyr C:222	-	Asp C:223
12	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:-2-26 B:-2-26 C:-2-26	29 29 29
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 B:304-361 C:304-361	58 58 58
1.10f	ENST00000313005	10f	ENSE00002041784	chr11:117160523-117156402	4122	BACE1_HUMAN	422-501	80	3	A:361-385 B:361-385 C:361-385	25 25 25

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:376
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:388
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        
          BACE1_HUMAN    59 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 446
               SCOP domains d1ym2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------1ym2A01 A:14-146 Acid Proteases                                                                                                      1ym2A02 A:1            47-385 Acid Proteases                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeee...eeeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee..------------.eeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh...............eee.....hhhhh..eeeeee.....eeeeeeehhhhheeee........eeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..hhhhhh.. 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:-2-26      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:361-38 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.4c  PDB: A:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: A:304-361 UniProt: 365-422                ------------------------ Transcript 1 (2)
                 1ym2 A  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGA------------VGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157         -  |    177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                                                                                                                                                                                         157          170

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

    Alignment length:388
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        
          BACE1_HUMAN    59 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 446
               SCOP domains d1ym2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------1ym2B01 B:14-146 Acid Proteases                                                                                                      1ym2B02 B:1           47-385 Acid Proteases                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eee.....eeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee..-----------.eeeeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eee.....hhhhh..eeeeee.....eeeeeeehhhhheee.........eeeee.eeee...eeehhhhhh.eeeeeehhh.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:361-38 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)
                 1ym2 B  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGA-----------SVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157         - |     177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                                                                                                                                                                                         157         169

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

    Alignment length:388
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        
          BACE1_HUMAN    59 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 446
               SCOP domains d1ym2c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------1ym2C01 C:14-146 Acid Proteases                                                                                                      1ym2C02 C:1            47-385 Acid Proteases                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeee...eeeeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee.......eeeee.eeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeee...------------..eeeee...hhh.eeeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh.......hhhhh...eee.....hhhhh..eeeee.......eeeeeehhhhheeee........eeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeee...hhhhhh.. 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:-2-26      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:361-38 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.4c  PDB: C:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: C:304-361 UniProt: 365-422                ------------------------ Transcript 1 (2)
                 1ym2 C  -2 SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGA------------VGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157         -  |    177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                                                                                                                                                                                         157          170

Chain X from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1ym2 X   1 xLMxVx   6
                            |  | |
                            1-ACE|
                               4-24O
                                 6-LYT

Chain Y from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1ym2 Y   1 xLMxVx   6
                            |  | |
                            |  | |
                            1-ACE|
                               4-24O
                                 6-LYT

Chain Z from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1ym2 Z   1 xLMxVx   6
                            |  | |
                            |  | |
                            1-ACE|
                               4-24O
                                 6-LYT

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	d1ym2a_	A:
1b	d1ym2b_	B:
1c	d1ym2c_	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	1ym2A01	A:14-146
1b	1ym2A02	A:147-385
1c	1ym2C02	C:147-385
1d	1ym2B02	B:147-385
1e	1ym2B01	B:14-146
1f	1ym2C01	C:14-146

(no "Pfam Domain" information available for 1YM2)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		24O	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LYT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	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 ]
		Gly B:372 - Pro B:373	[ RasMol ]
		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 ]
		Tyr A:222 - Asp A:223	[ RasMol ]
		Tyr B:222 - Asp B:223	[ RasMol ]
		Tyr C:222 - Asp C:223	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1ym2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BACE1_HUMAN \| P56817
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.23.46
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	BACE1_HUMAN \| P56817
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1ym4	BETA-SECRETASE COMPLEXED WITH NVP-AMK640

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (3, 3)

SS Bonds (9, 9)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

PROSITE Motifs (2, 6)

Exons (9, 27)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 6)

Pfam Domains (0, 0)

Gene Ontology (30, 30)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File