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- PDB-2djf: Crystal Structure of human dipeptidyl peptidase I (Cathepsin C) i... -

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Basic information

Entry
Database: PDB / ID: 2djf
TitleCrystal Structure of human dipeptidyl peptidase I (Cathepsin C) in complex with the inhibitor Gly-Phe-CHN2
Components(Dipeptidyl-peptidase ...) x 3
KeywordsHydrolase/Hydrolase inhibitor / protein-inhibitor complex / covalently bound inhibitor / DPPI-inhibitor complex / cathepsin C inhibitor complex / Hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / 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 / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1ZB / ACETIC ACID / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMolgaard, A. / Arnau, J. / Lauritzen, C. / Larsen, S. / Petersen, G. / Pedersen, J.
CitationJournal: Biochem.J. / Year: 2007
Title: The crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor Gly-Phe-CHN2
Authors: Molgaard, A. / Arnau, J. / Lauritzen, C. / Larsen, S. / Petersen, G. / Pedersen, J.
History
DepositionApr 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,80210
Polymers39,5753
Non-polymers1,2277
Water4,432246
1
A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,20840
Polymers158,30212
Non-polymers4,90628
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)87.000, 89.030, 115.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Dipeptidyl-peptidase ... , 3 types, 3 molecules ABC

#1: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 13500.163 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 exclusion domain chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 18491.871 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 7583.444 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 249 molecules

#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-1ZB / N-[(1S)-1-benzyl-3-diazen-1-iumylidene-2-oxopropyl]glycinamide


Type: peptide-like / Mass: 246.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23% PEG 4000, 0.22M ammonium acetate and 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.094 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2002 / Details: mirror and monochromator
RadiationMonochromator: Pt coated mirror plus Si(111) monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.094 Å / Relative weight: 1
ReflectionResolution: 2→28.75 Å / Num. obs: 143822
Reflection shellResolution: 2→2.07 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3B

1k3b


Resolution: 2→28.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.787 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20025 1549 5.1 %RANDOM
Rwork0.16126 ---
all0.16322 28953 --
obs0.16322 28953 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 77 246 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212914
X-RAY DIFFRACTIONr_bond_other_d0.0020.022449
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9483954
X-RAY DIFFRACTIONr_angle_other_deg0.85835690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023232
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02629
X-RAY DIFFRACTIONr_nbd_refined0.2040.2526
X-RAY DIFFRACTIONr_nbd_other0.2550.22776
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0561.51725
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92822760
X-RAY DIFFRACTIONr_scbond_it2.58531189
X-RAY DIFFRACTIONr_scangle_it4.1834.51194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.248 101
Rwork0.19 2072
obs-2072

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