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- PDB-1lam: LEUCINE AMINOPEPTIDASE (UNLIGATED) -

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Basic information

Entry
Database: PDB / ID: 1lam
TitleLEUCINE AMINOPEPTIDASE (UNLIGATED)
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
CARBONATE ION / Cytosol aminopeptidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.6 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 2.0Feb 14, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)53,2808
Polymers52,6691
Non-polymers6117
Water9,188510
1
A: LEUCINE AMINOPEPTIDASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)319,67848
Polymers316,0136
Non-polymers3,66542
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 area32860 Å2
ΔGint-768 kcal/mol
Surface area93040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.500, 131.500, 121.300
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 471
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-505-

HOH

31A-506-

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 (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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#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.: 510 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZN 488 AND ZN 489 ARE TWO CATALYTIC ZINC IONS IN THE ACTIVE SITE. ZN 490 IS A NON-CATALYTIC METAL ...ZN 488 AND ZN 489 ARE TWO CATALYTIC ZINC IONS IN THE ACTIVE SITE. ZN 490 IS A NON-CATALYTIC METAL ION. THE PRESENCE OF A CARBONATE ION BOUND NEAR ARG 336 IN THE ACTIVE SITE HAS BEEN CONCLUDED ON THE BASIS OF THE ELECTRON DENSITY MAPS. CARBONATE WAS NOT ADDED TO THE CRYSTALLIZATION SOLUTION. THREE MPD MOLECULES ARE BOUND TO THE PROTEIN SURFACE FROM THE CRYSTALLIZATION OR CRYOGENIC BUFFER. ALL MPD MOLECULES ARE MORE THAN 30 ANGSTROMS AWAY FROM THE ACTIVE SITE.

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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: 2.87 Å3/Da / Density % sol: 57.19 %
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 1, 1995
RadiationMonochromator: SUPPER DOUBLE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 76376 / % possible obs: 94.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 357105 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.6→7 Å / σ(F): 2
RfactorNum. reflection
Rfree0.204 -
Rwork0.172 -
obs0.172 73106
Displacement parametersBiso mean: 12.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 31 510 4240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_deg21.9
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.65 Å

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