1LYB - 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 STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN

Authors :   E. T. Baldwin, T. N. Bhat, S. Gulnik, J. W. Erickson

Date :   22 Apr 93 (Deposition) - 31 Jan 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,I,J
Biol. Unit 1: A (1x),B (1x),C (1x),D (1x),I (1x),J (1x)
Biol. Unit 2: A,B,I  (1x)
Biol. Unit 3: C,D,J  (1x)

Keywords :   Lysosomal Aspartic Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. T. Baldwin, T. N. Bhat, S. Gulnik, M. V. Hosur, R. C. Sowder 2Nd. , R. E. Cachau, J. Collins, A. M. Silva, J. W. Erickson
Crystal Structures Of Native And Inhibited Forms Of Human Cathepsin D: Implications For Lysosomal Targeting And Drug Design.
Proc. Natl. Acad. Sci. Usa V. 90 6796 1993
PubMed-ID: 8393577 | Reference-DOI: 10.1073/PNAS.90.14.6796
(for further references see the PDB file header)

Molecule 1 - CATHEPSIN D
	Chains	:	A, C
	EC Number	:	3.4.23.5
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	LIVER

Molecule 2 - CATHEPSIN D
	Chains	:	B, D
	EC Number	:	3.4.23.5
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	LIVER

Molecule 3 - PEPSTATIN
	Chains	:	I, J
	Engineered	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 16)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	IVA	2	Mod. Amino Acid	ISOVALERIC ACID
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	STA	4	Mod. Amino Acid	STATINE

Biological Unit 1 (5, 8)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	STA	2	Mod. Amino Acid	STATINE

Biological Unit 2 (5, 8)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	STA	2	Mod. Amino Acid	STATINE

Biological Unit 3 (5, 8)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	STA	2	Mod. Amino Acid	STATINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:199	BINDING SITE FOR RESIDUE NAG B 1
2	AC2	SOFTWARE	ASN D:199	BINDING SITE FOR RESIDUE NAG D 1
3	AC3	SOFTWARE	ASN A:70 , ASN B:145 , ASN B:146 , VAL B:147	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 70 RESIDUES 98 TO 101
4	AC4	SOFTWARE	ASN C:70 , ASN D:145 , ASN D:146	BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 70 RESIDUES 98 TO 101
5	AC5	SOFTWARE	ASP A:33 , GLY A:35 , SER A:36 , HIS A:77 , TYR A:78 , GLY A:79 , SER A:80 , TYR B:205 , ASP B:231 , GLY B:233 , THR B:234 , SER B:235 , ILE B:311	BINDING SITE FOR CHAIN I OF PEPSTATIN
6	AC6	SOFTWARE	ASP C:33 , GLY C:35 , SER C:36 , HIS C:77 , TYR C:78 , GLY C:79 , SER C:80 , TYR D:205 , ASP D:231 , GLY D:233 , THR D:234 , SER D:235 , LEU D:236 , GLU D:260	BINDING SITE FOR CHAIN J OF PEPSTATIN

Asymmetric Unit

No.	Residues
1	A:27	-	A:96
2	A:46	-	A:53
3	B:222	-	B:226
4	B:265	-	B:302
5	C:27	-	C:96
6	C:46	-	C:53
7	D:222	-	D:226
8	D:265	-	D:302

Asymmetric Unit

No.	Residues
1	Thr A:23	-	Pro A:24
2	Val A:94	-	Pro A:95
3	Gln B:176	-	Pro B:177
4	Pro B:313	-	Pro B:314
5	Gly B:316	-	Pro B:317
6	Gly C:1	-	Pro C:2
7	Thr C:23	-	Pro C:24
8	Val C:94	-	Pro C:95
9	Gln D:176	-	Pro D:177
10	Pro D:313	-	Pro D:314
11	Gly D:316	-	Pro D:317

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029362	F	229	I	CATD_HUMAN	Disease (CLN10)	121912789	B/D	F	165	I
2	UniProt	VAR_058490	G	282	R	CATD_HUMAN	Polymorphism	147278302	B/D	G	218	R
3	UniProt	VAR_029363	W	383	C	CATD_HUMAN	Disease (CLN10)	121912790	B/D	W	319	C

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029362	F	229	I	CATD_HUMAN	Disease (CLN10)	121912789	B/D	F	165	I
2	UniProt	VAR_058490	G	282	R	CATD_HUMAN	Polymorphism	147278302	B/D	G	218	R
3	UniProt	VAR_029363	W	383	C	CATD_HUMAN	Disease (CLN10)	121912790	B/D	W	319	C

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029362	F	229	I	CATD_HUMAN	Disease (CLN10)	121912789	B	F	165	I
2	UniProt	VAR_058490	G	282	R	CATD_HUMAN	Polymorphism	147278302	B	G	218	R
3	UniProt	VAR_029363	W	383	C	CATD_HUMAN	Disease (CLN10)	121912790	B	W	319	C

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

Biological Unit 3 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029362	F	229	I	CATD_HUMAN	Disease (CLN10)	121912789	D	F	165	I
2	UniProt	VAR_058490	G	282	R	CATD_HUMAN	Polymorphism	147278302	D	G	218	R
3	UniProt	VAR_029363	W	383	C	CATD_HUMAN	Disease (CLN10)	121912790	D	W	319	C

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.	CATD_HUMAN	79-407	2	A:15-97 C:15-97
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CATD_HUMAN	94-105 292-303	4	A:30-41 C:30-41 B:228-239 D:228-239

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CATD_HUMAN	79-407	2	A:15-97 C:15-97
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CATD_HUMAN	94-105 292-303	4	A:30-41 C:30-41 B:228-239 D:228-239

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.	CATD_HUMAN	79-407	1	A:15-97 -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CATD_HUMAN	94-105 292-303	2	A:30-41 - B:228-239 -

Biological Unit 3 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CATD_HUMAN	79-407	1	- C:15-97
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CATD_HUMAN	94-105 292-303	2	- C:30-41 - D:228-239

Asymmetric Unit (8, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000236671	1a	ENSE00001316045	chr11:1785222-1785022	201	CATD_HUMAN	1-23	23	0	-	-
1.3b	ENST00000236671	3b	ENSE00001612002	chr11:1782698-1782539	160	CATD_HUMAN	23-76	54	2	A:1-12 - C:1-12 -	12 - 12 -
1.4	ENST00000236671	4	ENSE00000690124	chr11:1780869-1780746	124	CATD_HUMAN	77-118	42	2	A:13-54 - C:13-54 -	42 - 42 -
1.5	ENST00000236671	5	ENSE00000690128	chr11:1780317-1780199	119	CATD_HUMAN	118-157	40	2	A:54-93 - C:54-93 -	40 - 40 -
1.6	ENST00000236671	6	ENSE00002178061	chr11:1778786-1778554	233	CATD_HUMAN	158-235	78	4	A:94-97 B:106-171 C:94-97 D:106-171	4 66 4 66
1.7b	ENST00000236671	7b	ENSE00002147820	chr11:1776258-1776136	123	CATD_HUMAN	235-276	42	2	- B:171-212 - D:171-212	- 42 - 42
1.8c	ENST00000236671	8c	ENSE00002179431	chr11:1775368-1775224	145	CATD_HUMAN	276-324	49	2	- B:212-260 - D:212-260	- 49 - 49
1.8f	ENST00000236671	8f	ENSE00002173924	chr11:1775131-1775033	99	CATD_HUMAN	325-357	33	2	- B:261-293 - D:261-293	- 33 - 33
1.9d	ENST00000236671	9d	ENSE00000794681	chr11:1774900-1773982	919	CATD_HUMAN	358-412	55	2	- B:294-346 - D:294-346	- 53 - 53

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:97
 aligned with CATD_HUMAN | P07339 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:97
                                    74        84        94       104       114       124       134       144       154       
           CATD_HUMAN    65 GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ 161
               SCOP domains d1lyb.1 A:,B: Cathepsin D                                                                         SCOP domains
               CATH domains 1lybA00 A:1-97 Acid Proteases                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeee...eeeeeeee....eeeeee...hhhhhhhhh............eeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: A:15-97 UniProt: 79-407                                          PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b   Exon 1.4  PDB: A:13-54 UniProt: 77-118    ---------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: A:54-93 UniProt: 118-157 ---- Transcript 1 (2)
                 1lyb A   1 GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ  97
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with CATD_HUMAN | P07339 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:241
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409 
           CATD_HUMAN   170 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 410
               SCOP domains d1lyb.1 A:,B: Cathepsin D                                                                                                                                                                                                                         SCOP domains
               CATH domains 1lybB00 B:106-346 Acid Proteases                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...hhhhhh.eeeeeee...........hhhhhhhhhhh....eeeeeee.......eeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..eeeee..eeeeee..eeeeeehhhhhhhhhhhhh.eee...eeeehhhhhhhh.eeeeee..eeeeehhhhhh....eee..eeeeeeeee............hhhhhh..eeeee..eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------I----------------------------------------------------R----------------------------------------------------------------------------------------------------C--------------------------- SAPs(SNPs)
                PROSITE (1) PEPTIDASE_A1  PDB: - UniProt: 79-407                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6  PDB: B:106-171 UniProt: 158-235 [INCOMPLETE]            ----------------------------------------Exon 1.8c  PDB: B:212-260 UniProt: 276-324       Exon 1.8f  PDB: B:261-293        Exon 1.9d  PDB: B:294-346 UniProt: 358-412            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.7b  PDB: B:171-212 UniProt: 235-276-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1lyb B 106 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 346
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain C from PDB  Type:PROTEIN  Length:97
 aligned with CATD_HUMAN | P07339 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:97
                                    74        84        94       104       114       124       134       144       154       
           CATD_HUMAN    65 GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ 161
               SCOP domains d1lyb.2 C:,D: Cathepsin D                                                                         SCOP domains
               CATH domains 1lybC00 C:1-97 Acid Proteases                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeee...eeeeeeee....eeeeee...hhhhhhhhh............eeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: C:15-97 UniProt: 79-407                                          PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b   Exon 1.4  PDB: C:13-54 UniProt: 77-118    ---------------------------------------1.6  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.5  PDB: C:54-93 UniProt: 118-157 ---- Transcript 1 (2)
                 1lyb C   1 GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ  97
                                    10        20        30        40        50        60        70        80        90

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with CATD_HUMAN | P07339 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:241
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409 
           CATD_HUMAN   170 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 410
               SCOP domains d1lyb.2 C:,D: Cathepsin D                                                                                                                                                                                                                         SCOP domains
               CATH domains 1lybD00 D:106-346 Acid Proteases                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) Asp-1lybD01 D:106-345                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) Asp-1lybD02 D:106-345                                                                                                                                                                                                                           - Pfam domains (2)
           Pfam domains (3) Asp-1lybD03 D:106-345                                                                                                                                                                                                                           - Pfam domains (3)
           Pfam domains (4) Asp-1lybD04 D:106-345                                                                                                                                                                                                                           - Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeee...hhhhhh.eeeeeee...........hhhhhhhhhhh....eeeeeee.......eeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..eeeee..eeeeee..eeeeeehhhhhhhhhhhhh.eee...eeeehhhhhhhh.eeeeee..eeeeehhhhhh....eee..eeeeeeeee............hhhhhh..eeeee..eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------I----------------------------------------------------R----------------------------------------------------------------------------------------------------C--------------------------- SAPs(SNPs)
                PROSITE (1) PEPTIDASE_A1  PDB: - UniProt: 79-407                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6  PDB: D:106-171 UniProt: 158-235 [INCOMPLETE]            ----------------------------------------Exon 1.8c  PDB: D:212-260 UniProt: 276-324       Exon 1.8f  PDB: D:261-293        Exon 1.9d  PDB: D:294-346 UniProt: 358-412            Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.7b  PDB: D:171-212 UniProt: 235-276-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1lyb D 106 GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA 346
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain I 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
                 1lyb I   1 xVVxAx   6
                            |  | |
                            1-IVA|
                               4-STA
                                 6-STA

Chain J 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
                 1lyb J   1 xVVxAx   6
                            |  | |
                            |  | |
                            1-IVA|
                               4-STA
                                 6-STA

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: Cathepsin D (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1lyb.1	A:,B:
1b	d1lyb.2	C:,D:

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	1lybA00	A:1-97
1b	1lybC00	C:1-97
1c	1lybB00	B:106-346
1d	1lybD00	D:106-346

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_AA (368)

Family: Asp (155)

Homo sapiens (Human) (116)

1a	Asp-1lybD01	D:106-345
1b	Asp-1lybD02	D:106-345
1c	Asp-1lybD03	D:106-345
1d	Asp-1lybD04	D:106-345

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CATD_HUMAN | P07339)

molecular function
	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:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue 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.
	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).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.

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	1lyb
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	CATD_HUMAN \| P07339	:	1lya 1lyw 4obz 4oc6 4od9

(no "Related Entries Specified in the PDB File" available for 1LYB)

Description

Compounds

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Ligands, Modified Residues, Ions (5, 16)

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SS Bonds (8, 8)

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