3C9E - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CATHEPSIN K : CHONDROITIN SULFATE COMPLEX.

Authors :   M. Kienetz, M. M. Cherney, M. N. G. James, D. Bromme

Date :   15 Feb 08 (Deposition) - 26 Aug 08 (Release) - 17 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   N:1 Cathepsin K : Chondroitin Sulfate Complex, "Beads-On-A-String" Organization, Hydrolase, Lysosome, Protease, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Li, M. Kienetz, M. M. Cherney, M. N. James, D. Bromme
The Crystal And Molecular Structures Of A Cathepsin K:Chondroitin Sulfate Complex.
J. Mol. Biol. V. 383 78 2008
PubMed-ID: 18692071 | Reference-DOI: 10.1016/J.JMB.2008.07.038

Molecule 1 - CATHEPSIN K
	Chains	:	A
	EC Number	:	3.4.22.38
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Gene	:	CTSK, CTSO, CTSO2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CATHEPSIN O, CATHEPSIN X, CATHEPSIN O2

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ASG	3	Ligand/Ion	2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
2	BDP	3	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
3	CA	1	Ligand/Ion	CALCIUM ION
4	E64	1	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	ASG	6	Ligand/Ion	2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
2	BDP	6	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
3	CA	-1	Ligand/Ion	CALCIUM ION
4	E64	2	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:9 , LYS A:10 , ASN A:190 , LYS A:191 , ASG A:302 , ASG A:306 , HOH A:443 , HOH A:463 , HOH A:531 , HOH A:549 , HOH A:597 , HOH A:598 , HOH A:675	BINDING SITE FOR RESIDUE BDP A 301
2	AC2	SOFTWARE	ARG A:8 , GLN A:172 , ASN A:190 , LEU A:195 , BDP A:301 , BDP A:303 , HOH A:414 , HOH A:426 , HOH A:437 , HOH A:444 , HOH A:493 , HOH A:655 , HOH A:675	BINDING SITE FOR RESIDUE ASG A 302
3	AC3	SOFTWARE	LYS A:9 , GLN A:172 , ASG A:302 , ASG A:304 , HOH A:421 , HOH A:461 , HOH A:494 , HOH A:510 , HOH A:640 , HOH A:656	BINDING SITE FOR RESIDUE BDP A 303
4	AC4	SOFTWARE	GLY A:170 , ILE A:171 , BDP A:303 , BDP A:305 , HOH A:461 , HOH A:483	BINDING SITE FOR RESIDUE ASG A 304
5	AC5	SOFTWARE	LYS A:9 , ASG A:304 , ASG A:306 , HOH A:495 , HOH A:547 , HOH A:611 , HOH A:665	BINDING SITE FOR RESIDUE BDP A 305
6	AC6	SOFTWARE	VAL A:5 , ASP A:6 , LYS A:10 , BDP A:301 , BDP A:305 , HOH A:443 , HOH A:495 , HOH A:597 , HOH A:633 , HOH A:665	BINDING SITE FOR RESIDUE ASG A 306
7	AC7	SOFTWARE	GLU A:59 , ASN A:70 , GLN A:73	BINDING SITE FOR RESIDUE CA A 307
8	AC8	SOFTWARE	GLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , GLU A:59 , ASN A:60 , GLY A:65 , GLY A:66 , TYR A:67 , LEU A:160 , ASN A:161 , HIS A:162 , HOH A:448 , HOH A:492 , HOH A:523 , HOH A:527 , HOH A:567 , HOH A:704	BINDING SITE FOR RESIDUE E64 A 308

Asymmetric Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:96
3	A:155	-	A:204

(no "Cis Peptide Bond" information available for 3C9E)

Asymmetric Unit (5, 5)

								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	R	8	P
2	UniProt	VAR_006725	G	146	R	CATK_HUMAN	Disease (PKND)	74315302	A	G	32	R
3	UniProt	VAR_015739	A	277	V	CATK_HUMAN	Disease (PKND)	74315304	A	A	163	V
4	UniProt	VAR_074024	Y	283	C	CATK_HUMAN	Disease (PKND)	---	A	Y	169	C
5	UniProt	VAR_006726	L	309	P	CATK_HUMAN	Disease (PKND)	29001685	A	L	195	P

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

Biological Unit 1 (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	R	8	P
2	UniProt	VAR_006725	G	146	R	CATK_HUMAN	Disease (PKND)	74315302	A	G	32	R
3	UniProt	VAR_015739	A	277	V	CATK_HUMAN	Disease (PKND)	74315304	A	A	163	V
4	UniProt	VAR_074024	Y	283	C	CATK_HUMAN	Disease (PKND)	---	A	Y	169	C
5	UniProt	VAR_006726	L	309	P	CATK_HUMAN	Disease (PKND)	29001685	A	L	195	P

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

Asymmetric Unit (3, 3)

	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	1	A:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_HUMAN	274-284	1	A:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_HUMAN	291-310	1	A:177-196

Biological Unit 1 (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:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_HUMAN	274-284	2	A:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_HUMAN	291-310	2	A:177-196

Asymmetric Unit (5, 5)

	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	1	A:1-19	19
1.6b	ENST00000271651	6b	ENSE00002193797	chr1:150776715-150776497	219	CATK_HUMAN	134-206	73	1	A:20-92	73
1.7	ENST00000271651	7	ENSE00001610479	chr1:150772185-150772020	166	CATK_HUMAN	207-262	56	1	A:93-148	56
1.8	ENST00000271651	8	ENSE00001602868	chr1:150771749-150771644	106	CATK_HUMAN	262-297	36	1	A:148-183	36
1.9	ENST00000271651	9	ENSE00000959757	chr1:150769374-150768684	691	CATK_HUMAN	297-329	33	1	A:183-215	33

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
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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 d3c9ea_ A: (Pro)cathepsin K                                                                                                                                                                                             SCOP domains
               CATH domains 3c9eA00 A:1-215 Cysteine proteinases                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............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:20-92 UniProt: 134-206                                 Exon 1.7  PDB: A:93-148 UniProt: 207-262                ----------------------------------Exon 1.9  PDB: A:183-215          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:148-183            -------------------------------- Transcript 1 (2)
                 3c9e A   1 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                                    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)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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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)

d3c9ea_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

Human (Homo sapiens) (92)

3c9eA00

A:1-215

(no "Pfam Domain" information available for 3C9E)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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Description

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Ligands, Modified Residues, Ions (4, 8)

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SS Bonds (3, 3)

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