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- PDB-1lyw: CATHEPSIN D AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1lyw
TitleCATHEPSIN D AT PH 7.5
Components(CATHEPSIN D) x 2
KeywordsASPARTIC PROTEASE / HYDROLASE / GLYCOPROTEIN
Function / homology
Function and homology information


cathepsin D / aspartic-type peptidase activity / insulin catabolic process / regulation of establishment of protein localization / lipoprotein catabolic process / execution phase of apoptosis / insulin receptor recycling / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins ...cathepsin D / aspartic-type peptidase activity / insulin catabolic process / regulation of establishment of protein localization / lipoprotein catabolic process / execution phase of apoptosis / insulin receptor recycling / Collagen degradation / autophagosome assembly / Metabolism of Angiotensinogen to Angiotensins / Insulin receptor recycling / MHC class II antigen presentation / lysosomal lumen / endosome lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / specific granule lumen / tertiary granule lumen / melanosome / peptidase activity / : / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / aspartic-type endopeptidase activity / lysosome / endosome membrane / positive regulation of apoptotic process / membrane raft / lysosomal membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Cathepsin D / Aspartic peptidase, N-terminal / A1 Propeptide / 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 ...Cathepsin D / Aspartic peptidase, N-terminal / A1 Propeptide / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, A.Y. / Gulnik, S.V. / Erickson, J.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Conformational switching in an aspartic proteinase.
Authors: Lee, A.Y. / Gulnik, S.V. / Erickson, J.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structures of Native and Inhibited Forms of Human Cathepsin D: Implications for Lysosomal Targeting and Drug Design
Authors: Baldwin, E.T. / Bhat, T.N. / Gulnik, S. / Hosur, M.V. / Sowder II, R.C. / Cachau, R.E. / Collins, J. / Silva, A.M. / Erickson, J.W.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Human Liver Cathepsin D. Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of a Lysosomal Enzyme
Authors: Gulnik, S. / Baldwin, E.T. / Tarasova, N. / Erickson, J.
History
DepositionJun 30, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN D
B: CATHEPSIN D
C: CATHEPSIN D
D: CATHEPSIN D
E: CATHEPSIN D
F: CATHEPSIN D
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,79012
Polymers147,8378
Non-polymers9534
Water10,052558
1
A: CATHEPSIN D
B: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1973
Polymers36,9592
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-31 kcal/mol
Surface area14600 Å2
MethodPISA
2
C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1973
Polymers36,9592
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-35 kcal/mol
Surface area14760 Å2
MethodPISA
3
E: CATHEPSIN D
F: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1973
Polymers36,9592
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-31 kcal/mol
Surface area14770 Å2
MethodPISA
4
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1973
Polymers36,9592
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-34 kcal/mol
Surface area14690 Å2
MethodPISA
5
E: CATHEPSIN D
F: CATHEPSIN D
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules

E: CATHEPSIN D
F: CATHEPSIN D
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,79012
Polymers147,8378
Non-polymers9534
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area38260 Å2
ΔGint-210 kcal/mol
Surface area48180 Å2
MethodPISA
6
A: CATHEPSIN D
B: CATHEPSIN D
C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules

A: CATHEPSIN D
B: CATHEPSIN D
C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,79012
Polymers147,8378
Non-polymers9534
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area38680 Å2
ΔGint-212 kcal/mol
Surface area48070 Å2
MethodPISA
7
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules

G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area16600 Å2
ΔGint-91 kcal/mol
Surface area26650 Å2
MethodPISA
8
A: CATHEPSIN D
B: CATHEPSIN D
C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-87 kcal/mol
Surface area26630 Å2
MethodPISA
9
E: CATHEPSIN D
F: CATHEPSIN D
hetero molecules

E: CATHEPSIN D
F: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area16500 Å2
ΔGint-81 kcal/mol
Surface area26690 Å2
MethodPISA
10
A: CATHEPSIN D
B: CATHEPSIN D
hetero molecules

A: CATHEPSIN D
B: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area16330 Å2
ΔGint-82 kcal/mol
Surface area26830 Å2
MethodPISA
11
E: CATHEPSIN D
F: CATHEPSIN D
G: CATHEPSIN D
H: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-83 kcal/mol
Surface area26950 Å2
MethodPISA
12
C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules

C: CATHEPSIN D
D: CATHEPSIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3956
Polymers73,9184
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area16770 Å2
ΔGint-86 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.256, 136.797, 140.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CATHEPSIN D


Mass: 10688.941 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: P07339, cathepsin D
#2: Protein
CATHEPSIN D


Mass: 26270.207 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / References: UniProt: P07339, cathepsin D
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATHEPSIN D IS FOUND PREDOMINANTLY IN A TWO-CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. ...CATHEPSIN D IS FOUND PREDOMINANTLY IN A TWO-CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. THE LIGHT CHAIN COMPRISES RESIDUES 1 - 97 AND THE HEAVY CHAIN COMPRISES RESIDUES 106 - 346.
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: 1.24 Å3/Da / Density % sol: 65 % / Description: DATA WAS COLLECTED USING 1 DEGREE OSCILLATION
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22 %(v/v)PEG4001reservoir
32.0 Mammonium sulfate1reservoir
4100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 197513 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 6.95
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.37 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2 / Rsym value: 0.318 / % possible all: 41
Reflection
*PLUS
Num. obs: 68982 / Num. measured all: 197513

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LYA

1lya


Resolution: 2.5→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: ALTHOUGH THERE ARE NO NON-CRYSTALLOGRAPHIC SYMMETRIC AXIES. WE DID NOT BOTHER TO LOCATE THEM. THEREFORE, NON-CRYSTALLOGRAPHIC SYMMETRY ARE NOT USED FOR OUR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 6380 10 %RANDOM
Rwork0.195 ---
obs0.195 63094 73 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 0 60 557 10945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.326 457 7.16 %
Rwork0.2635 3736 -
obs--42.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2SOL1.XPRMSOL1.XPRM
X-RAY DIFFRACTION3WATERPAR.DATWATERTOP.DAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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