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- PDB-2hd4: Crystal structure of proteinase K inhibited by a lactoferrin octa... -

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Basic information

Entry
Database: PDB / ID: 2hd4
TitleCrystal structure of proteinase K inhibited by a lactoferrin octapeptide Gly-Asp-Glu-Gln-Gly-Glu-Asn-Lys at 2.15 A resolution
Components
  • 8-mer Peptide from Lactotransferrin
  • Proteinase K
KeywordsHYDROLASE / proteinase K / complex / peptide complex / LACTOFERRIN FRAGMENT
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / Metal sequestration by antimicrobial proteins / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / peptidase K / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / humoral immune response / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / protein serine/threonine kinase activator activity / secretory granule / innate immune response in mucosa / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / antibacterial humoral response / heparin binding / positive regulation of NF-kappaB transcription factor activity / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin ...Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Lactotransferrin / Proteinase K / Lactotransferrin
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPrem Kumar, R. / Singh, A.K. / Singh, N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of proteinase K inhibited by a lactoferrin octapeptide Gly-Asp-Glu-Gln-Gly-Glu-Asn-Lys at 2.15 A resolution
Authors: Prem Kumar, R. / Singh, A.K. / Singh, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Proteinase K
B: 8-mer Peptide from Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9364
Polymers29,8362
Non-polymers1002
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.366, 68.366, 108.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Proteinase K / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Protein/peptide 8-mer Peptide from Lactotransferrin


Mass: 876.846 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).THIS PEPTIEDE WAS TRAPPED DURUNG ITS DIGESTION BY PROTEINASE K.
References: UniProt: Q8TCD2, UniProt: P02788*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate hydrate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 14558 / Num. obs: 14558 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.968 Å2 / Rsym value: 0.075 / Net I/σ(I): 7.1
Reflection shellResolution: 2.15→2.23 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7V

1p7v


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.441 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 729 5 %RANDOM
Rwork0.17066 ---
all0.17003 14493 --
obs0.17242 13764 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.925 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 1 262 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212223
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.943033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62224.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3131513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021759
X-RAY DIFFRACTIONr_nbd_refined0.1890.2976
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2203
X-RAY DIFFRACTIONr_metal_ion_refined0.0220.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.212
X-RAY DIFFRACTIONr_mcbond_it0.5061.51507
X-RAY DIFFRACTIONr_mcangle_it0.85422348
X-RAY DIFFRACTIONr_scbond_it1.4683823
X-RAY DIFFRACTIONr_scangle_it2.2264.5685
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 62 -
Rwork0.199 1001 -
obs--100 %

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