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- PDB-1lan: LEUCINE AMINOPEPTIDASE COMPLEX WITH L-LEUCINAL -

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Basic information

Entry
Database: PDB / ID: 1lan
TitleLEUCINE AMINOPEPTIDASE COMPLEX WITH L-LEUCINAL
ComponentsLEUCINE AMINOPEPTIDASE
KeywordsHYDROLASE (ALPHA-AMINOACYLPEPTIDE) / AMINOPEPTIDASE / EXOPEPTIDASE / METALLOPEPTIDASE
Function / homology
Function and homology information


cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / peptidase activity / manganese ion binding / mitochondrion ...cysteinylglycine-S-conjugate dipeptidase / prolyl aminopeptidase / leucyl aminopeptidase / dipeptidase activity / metalloaminopeptidase activity / carboxypeptidase activity / disordered domain specific binding / peptidase activity / manganese ion binding / mitochondrion / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Cytosol aminopeptidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsStraeter, N. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Two-metal ion mechanism of bovine lens leucine aminopeptidase: active site solvent structure and binding mode of L-leucinal, a gem-diolate transition state analogue, by X-ray crystallography.
Authors: Strater, N. / Lipscomb, W.N.
#1: Journal: Biochemistry / Year: 1995
Title: Transition State Analogue L-Leucinephosphonic Acid Bound to Bovine Lens Leucine Aminopeptidase: X-Ray Structure at 1.65 Angstroms Resolution in a New Crystal Form
Authors: Straeter, N. / Lipscomb, W.N.
#2: Journal: Adv.Enzymol.Relat.Areas Mol.Biol. / Year: 1994
Title: Structure and Mechanism of Bovine Lens Leucine Aminopeptidase
Authors: Kim, H. / Lipscomb, W.N.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Re-Refinement of the X-Ray Crystal Structure of Bovine Lens Leucine Aminopeptidase Complexed with Bestatin
Authors: Kim, H. / Burley, S.K. / Lipscomb, W.N.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Differentiation and Identification of the Two Catalytic Metal Binding Sites in Bovine Lens Leucine Aminopeptidase by X-Ray Crystallography
Authors: Kim, H. / Lipscomb, W.N.
#5: Journal: Biochemistry / Year: 1993
Title: X-Ray Crystallographic Determination of the Structure of Bovine Lens Leucine Aminopeptidase Complexed with Amastatin: Formulation of a Catalytic Mechanism Featuring a Gem-Diolate Transition State
Authors: Kim, H. / Lipscomb, W.N.
#6: Journal: J.Mol.Biol. / Year: 1992
Title: Structure Determination and Refinement of Bovine Lens Leucine Aminopeptidase and its Complex with Bestatin
Authors: Burley, S.K. / David, P.R. / Sweet, R.M. / Taylor, A. / Lipscomb, W.N.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Leucine Aminopeptidase: Bestatin Inhibition and a Model for Enzyme-Catalyzed Peptide Hydrolysis
Authors: Burley, S.K. / David, P.R. / Lipscomb, W.N.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Molecular Structure of Leucine Aminopeptidase at 2.7 Angstroms Resolution
Authors: Burley, S.K. / David, P.R. / Taylor, A. / Lipscomb, W.N.
History
DepositionAug 11, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3518
Polymers52,6691
Non-polymers6827
Water6,918384
1
A: LEUCINE AMINOPEPTIDASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)320,10548
Polymers316,0136
Non-polymers4,09242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area30350 Å2
ΔGint-306 kcal/mol
Surface area92730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.200, 131.200, 120.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: CIS PROLINE - PRO A 471
Components on special symmetry positions
IDModelComponents
11A-806-

HOH

21A-807-

HOH

31A-809-

HOH

41A-811-

HOH

51A-836-

HOH

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Components

#1: Protein LEUCINE AMINOPEPTIDASE / CYTOSOLIC AMINOPEPTIDASE


Mass: 52668.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: LENS / References: UniProt: P00727, leucyl aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlb1LAP1drop
20.050 mM1dropZnSO4
3200 mM1dropNaCl
450 mMTris-HCl1drop
550 mMTris-HCl1reservoir
60.050 mM1reservoirZnSO4/MPD

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jun 6, 1995
RadiationMonochromator: SUPPER DOUBLE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 44837 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 160257 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→7 Å / σ(F): 2
RfactorNum. reflection
Rfree0.212 -
Rwork0.168 -
obs0.168 42082
Displacement parametersBiso mean: 16.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 36 384 4119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_deg1.41
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å

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