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- PDB-1gvu: Endothiapepsin complex with H189 -

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Basic information

Entry
Database: PDB / ID: 1gvu
TitleEndothiapepsin complex with H189
Components
  • ENDOTHIAPEPSIN
  • INHIBITOR, H189Enzyme inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ASPARTIC PROTEINASE MECHANISM / ATOMIC RESOLUTION / Z TETRAHEDRAL INTERMEDIATE / ANISOTROPIC REFINEMENT / ASPARTYL P / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Peptide ligand-binding receptors / Metabolism of Angiotensinogen to Angiotensins / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / acrosome reaction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly ...Peptide ligand-binding receptors / Metabolism of Angiotensinogen to Angiotensins / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / acrosome reaction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly / calcium-ion regulated exocytosis / vasoconstriction / type 1 angiotensin receptor binding / positive regulation of extrinsic apoptotic signaling pathway / G alpha (q) signalling events / positive regulation of epidermal growth factor receptor signaling pathway / G alpha (i) signalling events / positive regulation of gap junction assembly / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / endothiapepsin / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / kidney development / angiotensin-activated signaling pathway / serine-type endopeptidase inhibitor activity / hormone activity / positive regulation of miRNA transcription / regulation of apoptotic process / aspartic-type endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / proteolysis / extracellular space
Similarity search - Function
Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors ...Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
H 189 / Angiotensinogen / Endothiapepsin
Similarity search - Component
Biological speciesENDOTHIA PARASITICA (chestnut blight fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.94 Å
AuthorsCoates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Five Atomic Resolution Structures of Endothiapepsin Inhibitor Complexes: Implications for the Aspartic Proteinase Mechanism
Authors: Coates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B.
History
DepositionFeb 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_src_syn / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOTHIAPEPSIN
I: INHIBITOR, H189
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2614
Polymers35,0682
Non-polymers1922
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-30 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.477, 75.779, 42.987
Angle α, β, γ (deg.)90.00, 95.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN / / ASPARTATE PROTEASE


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) ENDOTHIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Protein/peptide INHIBITOR, H189 / Enzyme inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 1272.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: H 189, UniProt: P01017*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: HYDROLYSIS OF PROTEINS SIMILAR TO PEPSIN A
Sequence detailsMODRES: 1GVU SUI A 54() ASP, GLY HAVE CYCLISED TO FORM A SUCCINIMIDE

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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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growpH: 4.5 / Details: PH 4.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 mg/mlenzyme11
2100 mMsodium acetate11

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 0.98→10 Å / Num. obs: 149856 / % possible obs: 99.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 5.2
Reflection shellResolution: 0.98→1.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 2.3 / % possible all: 100
Reflection
*PLUS
Highest resolution: 0.94 Å / Lowest resolution: 10 Å / Num. obs: 146980 / % possible obs: 86.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 0.94 Å / Lowest resolution: 0.99 Å / % possible obs: 72.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 0.94→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.139 7335 5.3 %RANDOM
all0.115 139281 --
obs0.116 -86.2 %-
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refinement stepCycle: LAST / Resolution: 0.94→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 10 462 2914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.1096 / Rfactor Rfree: 0.123
Solvent computation
*PLUS
Displacement parameters
*PLUS

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