1TU6 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CATHEPSIN K COMPLEXED WITH A KETOAMIDE INHIBITOR

Authors :   D. G. Barrett, J. G. Catalano, D. N. Deaton, A. M. Hassell, S. T. Long, A. B. Miller, L. R. Miller, L. M. Shewchuk, K. J. Wells-Knecht, L. L. Wright

Date :   24 Jun 04 (Deposition) - 21 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

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

Reference :   D. G. Barrett, J. G. Catalano, D. N. Deaton, A. M. Hassell, S. T. Long, A. B. Miller, L. R. Miller, L. M. Shewchuk, K. J. Wells-Knecht, D. H. Willard, L. L. Wright
Potent And Selective P2-P3 Ketoamide Inhibitors Of Cathepsin K With Improved Pharmacokinetic Properties Via Favorable P1', P1, And/Or P3 Substitutions
Bioorg. Med. Chem. Lett. V. 14 4897 2004
PubMed-ID: 15341947 | Reference-DOI: 10.1016/J.BMCL.2004.07.031
(for further references see the PDB file header)

Molecule 1 - CATHEPSIN K
	Chains	:	A, B
	EC Number	:	3.4.22.38
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector	:	PFASTBAC
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	CTSK, CTSO, CTSO2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CATHEPSIN O, CATHEPSIN X, CATHEPSIN O2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FSP	2	Ligand/Ion	[1-(4-FLUOROBENZYL)CYCLOBUTYL]METHYL (1S)-1-[OXO(1H-PYRAZOL-5-YLAMINO)ACETYL]PENTYLCARBAMATE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:132 , GLY A:299 , GLU A:300 , ASN A:301 , HOH A:576 , HOH A:682	BINDING SITE FOR RESIDUE SO4 A 441
2	AC2	SOFTWARE	LYS A:287 , HOH A:708 , HOH A:711 , HOH A:713 , LYS B:217 , LYS B:220 , HOH B:699	BINDING SITE FOR RESIDUE SO4 A 442
3	AC3	SOFTWARE	ARG A:237 , ARG B:225 , ARG B:241 , PHE B:326 , LYS B:328	BINDING SITE FOR RESIDUE SO4 B 443
4	AC4	SOFTWARE	GLN A:133 , GLY A:137 , SER A:138 , CYS A:139 , TRP A:140 , ASP A:175 , GLY A:178 , GLY A:179 , GLY A:180 , ALA A:248 , ASN A:275 , HIS A:276 , TRP A:298 , LEU A:323 , HOH A:578 , ASN B:132 , GLN B:135 , VAL B:204 , GLY B:205	BINDING SITE FOR RESIDUE FSP A 551
5	AC5	SOFTWARE	VAL A:204 , GLU A:208 , MET A:211 , SER A:252 , GLN B:133 , CYS B:136 , GLY B:137 , SER B:138 , CYS B:139 , TRP B:140 , GLY B:178 , GLY B:179 , GLY B:180 , ALA B:248 , LEU B:274 , ASN B:275 , HIS B:276 , TRP B:298 , LEU B:323 , HOH B:586 , HOH B:706	BINDING SITE FOR RESIDUE FSP B 561

Asymmetric/Biological Unit

No.	Residues
1	A:136	-	A:177
2	A:170	-	A:210
3	A:269	-	A:318
4	B:136	-	B:177
5	B:170	-	B:210
6	B:269	-	B:318

(no "Cis Peptide Bond" information available for 1TU6)

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074023	R	122	P	CATK_HUMAN	Disease (PKND)	---	A/B	R	122	P
2	UniProt	VAR_006725	G	146	R	CATK_HUMAN	Disease (PKND)	74315302	A/B	G	146	R
3	UniProt	VAR_015739	A	277	V	CATK_HUMAN	Disease (PKND)	74315304	A/B	A	277	V
4	UniProt	VAR_074024	Y	283	C	CATK_HUMAN	Disease (PKND)	---	A/B	Y	283	C
5	UniProt	VAR_006726	L	309	P	CATK_HUMAN	Disease (PKND)	29001685	A/B	L	309	P

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CATK_HUMAN	133-144	2	A:133-144 B:133-144
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_HUMAN	274-284	2	A:274-284 B:274-284
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_HUMAN	291-310	2	A:291-310 B:291-310

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000271651	1	ENSE00001343333	chr1:150780799-150780690	110	CATK_HUMAN	-	0	0	-	-
1.3a	ENST00000271651	3a	ENSE00001691906	chr1:150779282-150779162	121	CATK_HUMAN	1-40	40	0	-	-
1.4	ENST00000271651	4	ENSE00001044450	chr1:150778700-150778578	123	CATK_HUMAN	41-81	41	0	-	-
1.5	ENST00000271651	5	ENSE00001044471	chr1:150778492-150778337	156	CATK_HUMAN	82-133	52	2	A:115-133 B:115-133	19 19
1.6b	ENST00000271651	6b	ENSE00002193797	chr1:150776715-150776497	219	CATK_HUMAN	134-206	73	2	A:134-206 B:134-206	73 73
1.7	ENST00000271651	7	ENSE00001610479	chr1:150772185-150772020	166	CATK_HUMAN	207-262	56	2	A:207-262 B:207-262	56 56
1.8	ENST00000271651	8	ENSE00001602868	chr1:150771749-150771644	106	CATK_HUMAN	262-297	36	2	A:262-297 B:262-297	36 36
1.9	ENST00000271651	9	ENSE00000959757	chr1:150769374-150768684	691	CATK_HUMAN	297-329	33	2	A:297-329 B:297-329	33 33

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:215
 aligned with CATK_HUMAN | P43235 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:215
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           CATK_HUMAN   115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
               SCOP domains d1tu6a_ A: (Pro)cathepsin K                                                                                                                                                                                             SCOP domains
               CATH domains 1tu6A00 A:115-329 Cysteine proteinases                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------P-----------------------R----------------------------------------------------------------------------------------------------------------------------------V-----C-------------------------P-------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
           Transcript 1 (1) Exon 1.5           Exon 1.6b  PDB: A:134-206 UniProt: 134-206                               Exon 1.7  PDB: A:207-262 UniProt: 207-262               ----------------------------------Exon 1.9  PDB: A:297-329          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:262-297            -------------------------------- Transcript 1 (2)
                 1tu6 A 115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with CATK_HUMAN | P43235 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:215
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           CATK_HUMAN   115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
               SCOP domains d1tu6b_ B: (Pro)cathepsin K                                                                                                                                                                                             SCOP domains
               CATH domains 1tu6B00 B:115-329 Cysteine proteinases                                                                                                                                                                                  CATH domains
           Pfam domains (1) Peptidase_C1-1tu6B01 B:115-328                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) Peptidase_C1-1tu6B02 B:115-328                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------P-----------------------R----------------------------------------------------------------------------------------------------------------------------------V-----C-------------------------P-------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
           Transcript 1 (1) Exon 1.5           Exon 1.6b  PDB: B:134-206 UniProt: 134-206                               Exon 1.7  PDB: B:207-262 UniProt: 207-262               ----------------------------------Exon 1.9  PDB: B:297-329          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:262-297            -------------------------------- Transcript 1 (2)
                 1tu6 B 115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324

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: (Pro)cathepsin K (41)

Human (Homo sapiens) [TaxId: 9606] (40)

1a	d1tu6a_	A:
1b	d1tu6b_	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	1tu6A00	A:115-329
1b	1tu6B00	B:115-329

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Homo sapiens (Human) (45)

1a	Peptidase_C1-1tu6B01	B:115-328
1b	Peptidase_C1-1tu6B02	B:115-328

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CATK_HUMAN | P43235)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	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:0001968	fibronectin binding	Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
	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:0043394	proteoglycan binding	Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
	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:0045453	bone resorption	The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
	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:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0001957	intramembranous ossification	Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	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.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
	GO:0002224	toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0036021	endolysosome lumen	The volume enclosed by the membrane of an endolysosome. An endolysosome is a transient hybrid organelle formed by fusion of a late endosome with a lysosome.
	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: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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	1tu6
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(no "Related Entries Specified in the PDB File" available for 1TU6)

Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (6, 6)

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