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- PDB-27jo: Crystal structure of the mature form of human ASPRV1 bound to ind... -

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Basic information

Entry
Database: PDB / ID: 27jo
TitleCrystal structure of the mature form of human ASPRV1 bound to indinavir
ComponentsRetroviral-like aspartic protease 1
KeywordsHYDROLASE / Retroviral-like aspartic protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / skin development / protein processing / aspartic-type endopeptidase activity / membrane
Similarity search - Function
Retroviral-like aspartic protease 1 / gag-polyprotein putative aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY / Retroviral-like aspartic protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsChen, Z. / Feng, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2026
Title: Structure and enzymatic properties of human retroviral-like aspartic protease 1 and functional roles of disease-associated mutations.
Authors: Feng, X. / Chen, Z. / Lan, C. / Ding, J.
History
DepositionJun 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retroviral-like aspartic protease 1
B: Retroviral-like aspartic protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3603
Polymers29,7462
Non-polymers6141
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-12 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.934, 105.934, 55.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6

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Components

#1: Protein Retroviral-like aspartic protease 1 / Skin-specific retroviral-like aspartic protease / SASPase / Skin aspartic protease / TPA-inducible ...Skin-specific retroviral-like aspartic protease / SASPase / Skin aspartic protease / TPA-inducible aspartic proteinase-like protein / TAPS


Mass: 14873.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPRV1, SASP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53RT3, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-MK1 / N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE / INDINAVIR


Mass: 613.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H47N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.05 M calcium chloride dihydrate, 0.1 M MES monohydrate, pH 6.0, and 45% (v/v) PEG 200

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.08→52.9 Å / Num. obs: 21380 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.99 / Net I/σ(I): 22.5
Reflection shellResolution: 2.08→2.13 Å / Num. unique obs: 734 / CC1/2: 0.873

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Processing

SoftwareName: PHENIX / Version: 1.21.2_5419 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→52.9 Å / SU ML: 0.2873 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 1989 9.31 %
Rwork0.1968 19386 -
obs0.1997 21375 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.86 Å2
Refinement stepCycle: LAST / Resolution: 2.08→52.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 45 75 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651981
X-RAY DIFFRACTIONf_angle_d0.86562683
X-RAY DIFFRACTIONf_chiral_restr0.0602310
X-RAY DIFFRACTIONf_plane_restr0.0058336
X-RAY DIFFRACTIONf_dihedral_angle_d14.6234746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.32361430.29211390X-RAY DIFFRACTION99.8
2.13-2.190.34111350.26191354X-RAY DIFFRACTION100
2.19-2.250.30341470.23471390X-RAY DIFFRACTION99.93
2.26-2.330.28581360.2291357X-RAY DIFFRACTION100
2.33-2.410.27991410.24461384X-RAY DIFFRACTION100
2.41-2.510.29771420.23481366X-RAY DIFFRACTION100
2.51-2.620.2331390.2281382X-RAY DIFFRACTION100
2.62-2.760.28361370.21471381X-RAY DIFFRACTION100
2.76-2.930.23531410.24091385X-RAY DIFFRACTION100
2.93-3.160.24331430.22831378X-RAY DIFFRACTION100
3.16-3.480.22641480.20341384X-RAY DIFFRACTION99.93
3.48-3.980.22821460.18111401X-RAY DIFFRACTION100
3.98-5.010.16611450.14631397X-RAY DIFFRACTION100
5.01-52.90.20591460.17521437X-RAY DIFFRACTION99.81

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