3ZKM - 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)

Title :   BACE2 FAB COMPLEX

Authors :   D. W. Banner, A. Kuglstatter, J. Benz, M. Stihle, A. Ruf

Date :   23 Jan 13 (Deposition) - 29 May 13 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D,H,L
Biol. Unit 1: A,H,L  (1x)
Biol. Unit 2: B,C,D  (1x)

Keywords :   Hydrolase-Immune System Complex, Hydrolase, Aspartyl Protease/Fab Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. W. Banner, B. Gsell, J. Benz, J. Bertschinger, D. Burger, S. Brack, S. Cuppuleri, M. Debulpaep, A. Gast, D. Grabulovski, M. Hennig, H. Hilpert, W. Huber, A. Kuglstatter, E. Kusznir, T. Laeremans, H. Matile, C. Miscenic, A. Rufer, D. Schlatter, J. Steyeart, M. Stihle R. Thoma, M. Weber, A. Ruf
Mapping The Conformational Space Accessible To Bace2 Using Surface Mutants And Co-Crystals With Fab-Fragments, Fynomers, And Xaperones
Acta Crystallogr. , Sect. D V. 69 1124 2013
PubMed-ID: 23695257 | Reference-DOI: 10.1107/S0907444913006574

Molecule 1 - BETA-SECRETASE 2
	Chains	:	A, B
	EC Number	:	3.4.23.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR, RESIDUES 75-460
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ASPARTIC-LIKE PROTEASE 56 KDA, ASPARTYL PROTEASE 1, ASP1, ASP 1, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2, BETA- SITE APP CLEAVING ENZYME 2, DOWN REGION ASPARTIC PROTEASE, DRAP, M MEMAPSIN-1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1, THETA-SECRETASE BACE2

Molecule 2 - FAB HEAVY CHAIN
	Chains	:	H, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	HYBRIDOMA CELL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FAB LIGHT CHAIN
	Chains	:	L, D
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	HYBRIDOMA CELL
	Expression System Strain	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	HUMAN
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	H	L
Biological Unit 1 (1x)	:	A				H	L
Biological Unit 2 (1x)	:		B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	GOL	2	Ligand/Ion	GLYCEROL
3	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:98 , LEU A:112 , VAL A:113 , ASN A:114 , GLU A:150 , SER A:155	BINDING SITE FOR RESIDUE SO4 A1398
2	AC2	SOFTWARE	GLN A:279 , CYS A:282 , TRP A:283	BINDING SITE FOR RESIDUE DMS A1399
3	AC3	SOFTWARE	GLU B:98 , LEU B:112 , VAL B:113 , ASN B:114 , GLU B:150 , SER B:155	BINDING SITE FOR RESIDUE SO4 B1398
4	AC4	SOFTWARE	GLN B:279 , CYS B:282	BINDING SITE FOR RESIDUE DMS B1399
5	AC5	SOFTWARE	ARG C:38 , LYS C:43 , GLU C:46 , ALA C:62 , PHE C:63 , ARG C:66 , HOH C:2028	BINDING SITE FOR RESIDUE GOL C1217
6	AC6	SOFTWARE	ARG H:38 , LYS H:43 , GLU H:46 , ALA H:62 , PHE H:63 , ARG H:66 , HOH H:2027	BINDING SITE FOR RESIDUE GOL H1217

Asymmetric Unit

No.	Residues
1	A:230	-	A:395
2	A:282	-	A:331
3	B:171	-	B:371
4	B:230	-	B:395
5	B:282	-	B:331
6	C:22	-	C:95
7	C:143	-	C:198
8	D:23	-	D:92
9	D:138	-	D:198
10	H:22	-	H:95
11	H:143	-	H:198
12	L:23	-	L:92
13	L:138	-	L:198

Asymmetric Unit

No.	Residues
1	Thr A:38	-	Pro A:39
2	Lys A:144	-	Pro A:145
3	Gly A:384	-	Pro A:385
4	Thr B:38	-	Pro B:39
5	Lys B:144	-	Pro B:145
6	Gly B:384	-	Pro B:385
7	Phe C:149	-	Pro C:150
8	Glu C:151	-	Pro C:152
9	Trp C:191	-	Pro C:192
10	Ser D:7	-	Pro D:8
11	Asp D:80	-	Pro D:81
12	Asp D:98	-	Pro D:99
13	Tyr D:144	-	Pro D:145
14	Phe H:149	-	Pro H:150
15	Glu H:151	-	Pro H:152
16	Trp H:191	-	Pro H:192
17	Ser L:7	-	Pro L:8
18	Asp L:80	-	Pro L:81
19	Asp L:98	-	Pro L:99
20	Tyr L:144	-	Pro L:145

(no "SAP(SNP)/Variant" information available for 3ZKM)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	BACE2_HUMAN	92-429	2	A:30-367 B:30-367
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	BACE2_HUMAN	107-118 300-311	4	A:45-56 B:45-56 A:238-249 B:238-249

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	BACE2_HUMAN	92-429	1	A:30-367 -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	BACE2_HUMAN	107-118 300-311	2	A:45-56 - A:238-249 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	BACE2_HUMAN	92-429	1	- B:30-367
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	BACE2_HUMAN	107-118 300-311	2	- B:45-56 - B:238-249

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000330333	1	ENSE00001304779	chr21:42539728-42540502	775	BACE2_HUMAN	1-104	104	2	A:14-42 B:14-42	29 29
1.3a	ENST00000330333	3a	ENSE00001294412	chr21:42598193-42598281	89	BACE2_HUMAN	105-134	30	2	A:43-72 B:43-72	30 30
1.6	ENST00000330333	6	ENSE00001313528	chr21:42609440-42609656	217	BACE2_HUMAN	134-206	73	2	A:72-144 B:72-144	73 73
1.7d	ENST00000330333	7d	ENSE00001293136	chr21:42613746-42613874	129	BACE2_HUMAN	207-249	43	2	A:145-187 (gaps) B:145-187 (gaps)	43 43
1.8	ENST00000330333	8	ENSE00001315110	chr21:42615303-42615437	135	BACE2_HUMAN	250-294	45	2	A:188-232 B:188-232	45 45
1.9a	ENST00000330333	9a	ENSE00001299298	chr21:42617889-42617990	102	BACE2_HUMAN	295-328	34	2	A:233-266 B:233-266	34 34
1.10	ENST00000330333	10	ENSE00001319314	chr21:42622679-42622828	150	BACE2_HUMAN	329-378	50	2	A:267-316 B:267-316	50 50
1.12	ENST00000330333	12	ENSE00001297180	chr21:42629085-42629253	169	BACE2_HUMAN	379-435	57	2	A:317-373 B:317-373	57 57
1.13c	ENST00000330333	13c	ENSE00001820917	chr21:42647298-42648524	1227	BACE2_HUMAN	435-518	84	2	A:373-397 B:373-397	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:375
 aligned with BACE2_HUMAN | Q9Y5Z0 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:384
                                    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       455    
          BACE2_HUMAN    76 NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVP 459
               SCOP domains d3zkma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeee...eeeeeeee................................hhhhh...eeeeeeeeee....eeeeeeeeeeeee...................................hhhhh.......hhhhhhhhhhh...eeeeee...---------..eeeee...hhhhheeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh..........hhhhh.eee....hhhhh..eeeeee.....eeeeeeehhhhheee.......eeeeee.eeee...eeehhhhhh.eeeeee....eeeeee....ee..ee.eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:30-367 UniProt: 92-429                                                                                                                                                                                                                                                                                                       ------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:14-42       Exon 1.3a  PDB: A:43-72       ------------------------------------------------------------------------Exon 1.7d  PDB: A:145-187 (gaps)           Exon 1.8  PDB: A:188-232 UniProt: 250-294    Exon 1.9a  PDB: A:233-266         Exon 1.10  PDB: A:267-316 UniProt: 329-378        Exon 1.12  PDB: A:317-373 UniProt: 379-435               ------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.6  PDB: A:72-144 UniProt: 134-206                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:373-39 Transcript 1 (2)
                 3zkm A  14 NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGA---------NGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVP 397
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    
                                                                                                                                                                                         173       183

Chain B from PDB  Type:PROTEIN  Length:375
 aligned with BACE2_HUMAN | Q9Y5Z0 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:384
                                    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       455    
          BACE2_HUMAN    76 NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVP 459
               SCOP domains d3zkmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..eeee...eeeeeeee................................hhhhh...eeeeeeeeee....eeeeeeeeeeeee...................................hhhhh.......hhhhhhhhhhh...eeeeee...---------..eeeee...hhhhheeeeeeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh..........hhhhh.eee....hhhhh..eeeeee.....eeeeeeehhhhheee.......eeeeee.eeee...eeehhhhhh.eeeeee....eeeeee....ee..ee.eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: B:30-367 UniProt: 92-429                                                                                                                                                                                                                                                                                                       ------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:14-42       Exon 1.3a  PDB: B:43-72       ------------------------------------------------------------------------Exon 1.7d  PDB: B:145-187 (gaps)           Exon 1.8  PDB: B:188-232 UniProt: 250-294    Exon 1.9a  PDB: B:233-266         Exon 1.10  PDB: B:267-316 UniProt: 329-378        Exon 1.12  PDB: B:317-373 UniProt: 379-435               ------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.6  PDB: B:72-144 UniProt: 134-206                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: B:373-39 Transcript 1 (2)
                 3zkm B  14 NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGA---------NGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVP 397
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    
                                                                                                                                                                                         173       183

Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zkm C   1 xVQLKESGPVLVAPSQSLFISCTVSGFSLTRYGVHWVRQSPGKGLEWLGVIWAGGTTNYNSAFMSRLTISKDNSKSQVFLKMNSLQTDDTAIYYCVKAYRNAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 217
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                            1-PCA

Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d3zkmd1 D:1-111 automated matches                                                                              d3zkmd2 D:112-217 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zkm D   1 NIVLSQSPGSLAVSLGQRATISCRASKSVDTYGHSFIHWYQQKPGQPPNLLIHLASNLESGVPARFSGRGSGTDFTLTIDPVEADDAATYYCQQNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eeehhhhhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zkm H   1 xVQLKESGPVLVAPSQSLFISCTVSGFSLTRYGVHWVRQSPGKGLEWLGVIWAGGTTNYNSAFMSRLTISKDNSKSQVFLKMNSLQTDDTAIYYCVKAYRNAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 217
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                            1-PCA

Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d3zkml1 L:1-111 automated matches                                                                              d3zkml2 L:112-217 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zkm L   1 NIVLSQSPGSLAVSLGQRATISCRASKSVDTYGHSFIHWYQQKPGQPPNLLIHLASNLESGVPARFSGRGSGTDFTLTIDPVEADDAATYYCQQNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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: automated matches (23)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d3zkma_	A:
1b	d3zkmb_	B:

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

2a	d3zkmd1	D:1-111
2b	d3zkml1	L:1-111

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

3a	d3zkmd2	D:112-217
3b	d3zkml2	L:112-217

(no "CATH Domain" information available for 3ZKM)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BACE2_HUMAN | Q9Y5Z0)

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: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.
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:0006509	membrane protein ectodomain proteolysis	The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
	GO:0042985	negative regulation of amyloid precursor protein biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta.
	GO:0016486	peptide hormone processing	The generation of a mature peptide hormone by posttranslational processing of a prohormone.
	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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
		Asp D:80 - Pro D:81	[ RasMol ]
		Asp D:98 - Pro D:99	[ RasMol ]
		Asp L:80 - Pro L:81	[ RasMol ]
		Asp L:98 - Pro L:99	[ RasMol ]
		Glu C:151 - Pro C:152	[ RasMol ]
		Glu H:151 - Pro H:152	[ RasMol ]
		Gly A:384 - Pro A:385	[ RasMol ]
		Gly B:384 - Pro B:385	[ RasMol ]
		Lys A:144 - Pro A:145	[ RasMol ]
		Lys B:144 - Pro B:145	[ RasMol ]
		Phe C:149 - Pro C:150	[ RasMol ]
		Phe H:149 - Pro H:150	[ RasMol ]
		Ser D:7 - Pro D:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr A:38 - Pro A:39	[ RasMol ]
		Thr B:38 - Pro B:39	[ RasMol ]
		Trp C:191 - Pro C:192	[ RasMol ]
		Trp H:191 - Pro H:192	[ RasMol ]
		Tyr D:144 - Pro D:145	[ RasMol ]
		Tyr L:144 - Pro L:145	[ RasMol ]

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Access by PDB/NDB ID
	3zkm
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	BACE2_HUMAN \| Q9Y5Z0
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	3.4.23.45
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UniProtKB/Swiss-Prot
	BACE2_HUMAN \| Q9Y5Z0	:	2ewy 3zkg 3zki 3zkn 3zkq 3zks 3zkx 3zl7 3zlq 4bel 4bfb

3zkg	BACE2 MUTANT APO STRUCTURE
3zki	BACE2 MUTANT STRUCTURE WITH LIGAND
3zkn	BACE2 FAB INHIBITOR COMPLEX
3zkq	BACE2 XAPERONE COMPLEX
3zkx	TERNARY BACE2 XAPERONE COMPLEX
3zl7	BACE2 FYNOMER COMPLEX
3zov	CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (13, 13)

Cis Peptide Bonds (20, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (9, 18)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File