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Basic information

Entry
Database: PDB / ID: 3h7d
TitleThe crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate
ComponentsCathepsin K
KeywordsHYDROLASE / glycosaminoglycan / sulfhydryl peptidase / cathepsin K mutant / ternary complex / Disease mutation / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen
Function / homology
Function and homology information


cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process ...cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / bone resorption / mitophagy / collagen binding / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / lysosome / apical plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / extracellular region / nucleoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-E64 / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.242 Å
AuthorsCherney, M.M. / Kienetz, M. / Bromme, D. / James, M.N.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure-activity analysis of cathepsin K/chondroitin 4-sulfate interactions.
Authors: Cherney, M.M. / Lecaille, F. / Kienitz, M. / Nallaseth, F.S. / Li, Z. / James, M.N. / Bromme, D.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin K
E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1167
Polymers46,9192
Non-polymers2,1975
Water4,648258
1
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2564
Polymers23,4591
Non-polymers1,7973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8603
Polymers23,4591
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cathepsin K
hetero molecules

A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5128
Polymers46,9192
Non-polymers3,5936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5540 Å2
ΔGint22 kcal/mol
Surface area19490 Å2
MethodPISA
4
E: Cathepsin K
hetero molecules

E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7206
Polymers46,9192
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.564, 42.014, 87.509
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-300-

CA

21E-300-

CA

31A-258-

HOH

Detailsmonomer

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Components

#1: Protein Cathepsin K / Cathepsin O / Cathepsin X / Cathepsin O2


Mass: 23459.307 Da / Num. of mol.: 2 / Fragment: UNP residues 115-329 / Mutation: K9E, I171E, Q172S, N190M, K191G, L195K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K
#2: Polysaccharide 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2- ...2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1396.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-3DGalpNAc[4S]b1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122A-1b_1-5][a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-3-deoxy-GalpNAc4SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE OLIGOSACCHARIDE CHAIN (BDP-ASG)N IS CONTINUOUS. IT IS RUNNING THROUGH THE SEVERAL UNIT CELLS. ...THE OLIGOSACCHARIDE CHAIN (BDP-ASG)N IS CONTINUOUS. IT IS RUNNING THROUGH THE SEVERAL UNIT CELLS. ONLY A HEXASACCHARIDE IN EACH ASYMMETRIC UNIT CAN BE SEEN. THERE ARE DISORDERED PARTS BETWEEN HEXASACCHARIDES THAT WERE NOT MODELED. O3 ATOM OF ASG 221 IS ALSO LACKING DENSITY TO PLACE IT CORRECTLY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 24791 / Num. obs: 24692 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.4_4)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATK

1atk


Resolution: 2.242→40.245 Å / SU ML: 0.9 / σ(F): 1.34 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2377 1256 5.09 %
Rwork0.1774 --
obs0.1805 24685 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.713 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2954 Å2-0 Å22.1239 Å2
2---6.4414 Å2-0 Å2
3---2.146 Å2
Refinement stepCycle: LAST / Resolution: 2.242→40.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 142 258 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073507
X-RAY DIFFRACTIONf_angle_d1.0734739
X-RAY DIFFRACTIONf_dihedral_angle_d18.3661332
X-RAY DIFFRACTIONf_chiral_restr0.071468
X-RAY DIFFRACTIONf_plane_restr0.008616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2419-2.33170.31531280.22712462X-RAY DIFFRACTION95
2.3317-2.43780.2561280.19962563X-RAY DIFFRACTION99
2.4378-2.56630.28161420.18822558X-RAY DIFFRACTION99
2.5663-2.7270.29931330.18862604X-RAY DIFFRACTION100
2.727-2.93750.2271470.16862633X-RAY DIFFRACTION100
2.9375-3.2330.24251380.15892622X-RAY DIFFRACTION100
3.233-3.70060.19821490.14652599X-RAY DIFFRACTION100
3.7006-4.66120.1791340.13632672X-RAY DIFFRACTION100
4.6612-40.25190.24871570.20452716X-RAY DIFFRACTION100

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