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- PDB-8pch: CRYSTAL STRUCTURE OF PORCINE CATHEPSIN H DETERMINED AT 2.1 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 8pch
TitleCRYSTAL STRUCTURE OF PORCINE CATHEPSIN H DETERMINED AT 2.1 ANGSTROM RESOLUTION: LOCATION OF THE MINI-CHAIN C-TERMINAL CARBOXYL GROUP DEFINES CATHEPSIN H AMINOPEPTIDASE FUNCTION
Components(CATHEPSIN H) x 2
KeywordsHYDROLASE / PROTEASE / CYSTEINE PROTEINASE / AMINOPEPTIDASE
Function / homology
Function and homology information


cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / alveolar lamellar body / thyroid hormone binding / immune response-regulating signaling pathway / membrane protein proteolysis / lysosomal protein catabolic process ...cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / alveolar lamellar body / thyroid hormone binding / immune response-regulating signaling pathway / membrane protein proteolysis / lysosomal protein catabolic process / bradykinin catabolic process / Neutrophil degranulation / metanephros development / surfactant homeostasis / cellular response to thyroid hormone stimulus / zymogen activation / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of epithelial cell migration / response to retinoic acid / aminopeptidase activity / ERK1 and ERK2 cascade / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / protein destabilization / cytoplasmic ribonucleoprotein granule / endopeptidase activity / lysosome / immune response / positive regulation of cell migration / serine-type endopeptidase activity / cysteine-type endopeptidase activity / positive regulation of gene expression / proteolysis / extracellular space / cytosol
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
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGuncar, G. / Podobnik, M. / Pungercar, J. / Strukelj, B. / Turk, V. / Turk, D.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of porcine cathepsin H determined at 2.1 A resolution: location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function.
Authors: Guncar, G. / Podobnik, M. / Pungercar, J. / Strukelj, B. / Turk, V. / Turk, D.
History
DepositionNov 7, 1997Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATHEPSIN H
P: CATHEPSIN H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7643
Polymers25,1772
Non-polymers5871
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint6 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.442, 68.730, 86.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CATHEPSIN H


Mass: 24328.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: SPLEEN / References: UniProt: O46427, cathepsin H
#2: Protein/peptide CATHEPSIN H


Mass: 848.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: SPLEEN / References: UniProt: O46427*PLUS, cathepsin H
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.8
Details: PROTEIN WAS CRYSTALLIZED USING SITTING DROP VAPOR DIFFUSION METHOD FROM 0.05M NA-ACETATE AND 5% MME PEG 5K BUFFER, PH 4.8. CONCENTRATION OF APPLIED PROTEIN WAS 11 MG/ML., vapor diffusion - sitting drop
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
220 mMsodium acetate1drop
31 mMEDTA1drop
40.05 Msodium acetate1reservoir
55 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.98 Å / Num. obs: 15946 / % possible obs: 95 % / Observed criterion σ(I): 1 / Rsym value: 0.118
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 99 Å / % possible obs: 98 % / Num. measured all: 102384 / Rmerge(I) obs: 0.11

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MAINmodel building
MAINrefinement
MAINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACT

2act


Resolution: 2.1→8 Å / Cross valid method: R-FREE,KICKED OMIT MAP / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.245 1308 10 %
obs-12932 98.1 %
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 39 179 1982
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.53

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