1M6D - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN CATHEPSIN F

Authors :   J. R. Somoza, J. T. Palmer, J. D. Ho

Date :   15 Jul 02 (Deposition) - 15 Jul 03 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Papain Family Cysteine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Somoza, J. T. Palmer, J. D. Ho
The Crystal Structure Of Human Cathepsin F And Its Implications For The Development Of Novel Immunomodulators
J. Mol. Biol. V. 322 559 2002
PubMed-ID: 12225749 | Reference-DOI: 10.1016/S0022-2836(02)00780-5

Molecule 1 - CATHEPSIN F
	Chains	:	A, B
	EC Number	:	3.4.22.41
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC9
	Expression System Strain	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	CATF
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CATSF

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MYP	2	Ligand/Ion	4-MORPHOLIN-4-YL-PIPERIDINE-1-CARBOXYLIC ACID [1-(3-BENZENESULFONYL-1-PROPYL-ALLYLCARBAMOYL)-2-PHENYLETHYL]-AMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:19 , GLY A:23 , CYS A:25 , TRP A:26 , GLY A:65 , GLY A:66 , LEU A:67 , GLN A:142 , LEU A:152B , SER A:154 , PRO A:156A , LEU A:156B , ILE A:157 , ASP A:158 , HIS A:159 , TRP A:177 , HOH A:1302 , HOH A:1312 , TRP B:156 , PRO B:156A , HOH B:2292	BINDING SITE FOR RESIDUE MYP A 1280
2	AC2	SOFTWARE	SER A:73 , ASN A:78 , GLN B:19 , GLY B:23 , CYS B:25 , TRP B:26 , MET B:64 , GLY B:65 , GLY B:66 , LEU B:67 , ALA B:133 , PHE B:143 , ILE B:157 , ASP B:158 , HIS B:159 , TRP B:177 , MET B:205 , HOH B:2365 , HOH B:2380 , HOH B:2399	BINDING SITE FOR RESIDUE MYP B 2280

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:95
3	A:153A	-	A:200
4	B:22	-	B:63
5	B:56	-	B:95
6	B:153A	-	B:200

(no "Cis Peptide Bond" information available for 1M6D)

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_070160	Q	321	R	CATF_HUMAN	Disease (CLN13)	397514731	A/B	Q	51	R
2	UniProt	VAR_070161	G	458	A	CATF_HUMAN	Disease (CLN13)	397514732	A/B	G	182	A
3	UniProt	VAR_070162	S	480	L	CATF_HUMAN	Disease (CLN13)	397514733	A/B	S	208	L

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CATF_HUMAN	289-300	2	A:19-30 B:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATF_HUMAN	429-439	2	A:157-167 B:157-167

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000310325	2	ENSE00001188380	chr11:66336067-66335745	323	CATF_HUMAN	1-71	71	0	-	-
1.3	ENST00000310325	3	ENSE00001188376	chr11:66335553-66335455	99	CATF_HUMAN	72-104	33	0	-	-
1.4c	ENST00000310325	4c	ENSE00001188372	chr11:66335133-66334915	219	CATF_HUMAN	105-177	73	0	-	-
1.5a	ENST00000310325	5a	ENSE00001233025	chr11:66334792-66334717	76	CATF_HUMAN	178-203	26	0	-	-
1.6b	ENST00000310325	6b	ENSE00001188359	chr11:66333875-66333762	114	CATF_HUMAN	203-241	39	0	-	-
1.7a	ENST00000310325	7a	ENSE00001188356	chr11:66333638-66333493	146	CATF_HUMAN	241-289	49	2	A:1-19 B:1-19	19 19
1.8a	ENST00000310325	8a	ENSE00001188351	chr11:66333398-66333302	97	CATF_HUMAN	290-322	33	2	A:20-52 B:20-52	33 33
1.8c	ENST00000310325	8c	ENSE00001188349	chr11:66333222-66333142	81	CATF_HUMAN	322-349	28	2	A:52-78B (gaps) B:52-78B (gaps)	29 29
1.9a	ENST00000310325	9a	ENSE00001188347	chr11:66332477-66332358	120	CATF_HUMAN	349-389	41	2	A:78B-119 (gaps) B:78B-119 (gaps)	43 43
1.9c	ENST00000310325	9c	ENSE00001188342	chr11:66332277-66332213	65	CATF_HUMAN	389-410	22	2	A:119-142 (gaps) B:119-142 (gaps)	24 24
1.10b	ENST00000310325	10b	ENSE00001233018	chr11:66332119-66332029	91	CATF_HUMAN	411-441	31	2	A:143-167B (gaps) B:143-167B (gaps)	33 33
1.10e	ENST00000310325	10e	ENSE00001188333	chr11:66331617-66331559	59	CATF_HUMAN	441-460	20	2	A:167B-184 B:167B-184	20 20
1.11b	ENST00000310325	11b	ENSE00002162432	chr11:66331478-66330934	545	CATF_HUMAN	461-484	24	2	A:185-212 (gaps) B:185-212 (gaps)	28 28

Asymmetric/Biological 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:214
 aligned with CATF_HUMAN | Q9UBX1 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:214
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    
          CATF_HUMAN    271 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCNFSAEKAKVYINDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGNRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD  484
               SCOP domains d1m6da_ A: Cathepsin F                                                                                                                                                                                                 SCOP domains
               CATH domains 1m6dA00 A:1-212 Cysteine proteinases                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...................hhhhh.....eeee...hhhhhhhhhhhhh.eeeee.hhhhhhh...ee..hhhhh...................eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------A---------------------L---- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7a          Exon 1.8a  PDB: A:20-52          --------------------------Exon 1.9a  PDB: A:78B-119 (gaps)         ---------------------Exon 1.10b UniProt: 411-441    -------------------Exon 1.11b               Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.8c UniProt: 322-349  ---------------------------------------Exon 1.9c             ------------------------------Exon 1.10e          ------------------------ Transcript 1 (2)
                1m6d A    1 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCQFSAEKAKVYIQDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGQRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD  212
                                    10        20        30        40        50        60        70     |||79        89||      99   ||  110       120       130     ||142      154A||||   158      167A|||    174       184       198       208    
                                                                                                      76|||         89A|         103|                            136|       149| |||||   |        167A|||                       193|              
                                                                                                       78||           91          105                             139        152 |||||   |         167B||                        198              
                                                                                                       78A|                                                                   154A||||   |          167C|                                         
                                                                                                        78B                                                                    155A|||   |           167D                                         
                                                                                                                                                                                156A||   |                                                        
                                                                                                                                                                                 152B|   |                                                        
                                                                                                                                                                                  153A   |                                                        
                                                                                                                                                                                      156B

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with CATF_HUMAN | Q9UBX1 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:214
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    
          CATF_HUMAN    271 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCNFSAEKAKVYINDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGNRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD  484
               SCOP domains d1m6db_ B: Cathepsin F                                                                                                                                                                                                 SCOP domains
               CATH domains 1m6dB00 B:1-212 Cysteine proteinases                                                                                                                                                                                   CATH domains
           Pfam domains (1) Peptidase_C1-1m6dB01 B:1-210                                                                                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-1m6dB02 B:1-210                                                                                                                                                                                        -- Pfam domains (2)
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...........................eeeeee...hhhhhhhhhhhhh.eeeeehhhhh......ee..hhhhhhhhhh..............eeeeeee...........eeeee...hhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------A---------------------L---- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7a          Exon 1.8a  PDB: B:20-52          --------------------------Exon 1.9a  PDB: B:78B-119 (gaps)         ---------------------Exon 1.10b UniProt: 411-441    -------------------Exon 1.11b               Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.8c UniProt: 322-349  ---------------------------------------Exon 1.9c             ------------------------------Exon 1.10e          ------------------------ Transcript 1 (2)
                1m6d B    1 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCQFSAEKAKVYIQDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGQRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD  212
                                    10        20        30        40        50        60        70     |||79        89||      99   ||  110       120       130     ||142      154A||||   158      167A|||    174       184       198       208    
                                                                                                      76|||         89A|         103|                            136|       149| |||||   |        167A|||                       193|              
                                                                                                       78||           91          105                             139        152 |||||   |         167B||                        198              
                                                                                                       78A|                                                                   154A||||   |          167C|                                         
                                                                                                        78B                                                                    155A|||   |           167D                                         
                                                                                                                                                                                156A||   |                                                        
                                                                                                                                                                                 152B|   |                                                        
                                                                                                                                                                                  153A   |                                                        
                                                                                                                                                                                      156B

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: Cathepsin F (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1m6da_	A:
1b	d1m6db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

Human (Homo sapiens) (92)

1a	1m6dA00	A:1-212
1b	1m6dB00	B:1-212

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Homo sapiens (Human) (45)

1a	Peptidase_C1-1m6dB01	B:1-210
1b	Peptidase_C1-1m6dB02	B:1-210

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CATF_HUMAN | Q9UBX1)

molecular function
	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:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of 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.
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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051603	proteolysis involved in cellular protein catabolic process	The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
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: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:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1M6D)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (6, 6)

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