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- PDB-1lcp: BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSP... -

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Basic information

Entry
Database: PDB / ID: 1lcp
TitleBOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSPHONIC ACID
ComponentsLEUCINE AMINOPEPTIDASE
KeywordsHYDROLASE (ALPHA-AMINOACYLPEPTIDE)
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 PHOSPHONIC ACID / Cytosol aminopeptidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsStraeter, N. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Transition state analogue L-leucinephosphonic acid bound to bovine lens leucine aminopeptidase: X-ray structure at 1.65 A resolution in a new crystal form.
Authors: Strater, N. / Lipscomb, W.N.
#1: Journal: Adv.Enzymol.Relat.Areas Mol.Biol. / Year: 1994
Title: Structure and Mechanism of Bovine Lens Leucine Aminopeptidase
Authors: Kim, H. / Lipscomb, W.N.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Jul 31, 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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
B: LEUCINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,77316
Polymers105,3382
Non-polymers1,43614
Water17,439968
1
A: LEUCINE AMINOPEPTIDASE
B: LEUCINE AMINOPEPTIDASE
hetero molecules

A: LEUCINE AMINOPEPTIDASE
B: LEUCINE AMINOPEPTIDASE
hetero molecules

A: LEUCINE AMINOPEPTIDASE
B: LEUCINE AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,32048
Polymers316,0136
Non-polymers4,30742
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area34260 Å2
ΔGint-831 kcal/mol
Surface area93770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.400, 130.400, 125.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: CIS PROLINE - PRO A 471 / 2: CIS PROLINE - PRO B 471
Components on special symmetry positions
IDModelComponents
11B-652-

HOH

21B-790-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998453, -0.054621, 0.010423), (-0.054646, 0.998503, -0.002188), (-0.010288, -0.002188, -0.999943)
Vector: 3.8875, 0.1337, 65.0845)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. 484 A 1 .. 484 0.218 SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: A 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 1 -0.500000 -0.866025 0.000000 65.15000 SYMMETRY2 1 0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: A 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 2 -0.500000 0.866025 0.000000 -65.15000 SYMMETRY2 2 -0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: B 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 1 -0.500000 -0.866025 0.000000 65.15000 SYMMETRY2 1 0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: B 1 .. 490 1 OF 4 TRANSFORMATIONS TO GENERATE ONE HEXAMER OF 32 SYMMETRY. SYMMETRY1 2 -0.500000 0.866025 0.000000 -65.15000 SYMMETRY2 2 -0.866025 -0.500000 0.000000 112.84310 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein LEUCINE AMINOPEPTIDASE


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


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PLU / LEUCINE PHOSPHONIC ACID


Mass: 167.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO3P
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURE ASSIGNMENT IS TAKEN FROM REFERENCE 3. THERE ARE NO SIGNIFICANT DEVIATIONS ...THE SECONDARY STRUCTURE ASSIGNMENT IS TAKEN FROM REFERENCE 3. THERE ARE NO SIGNIFICANT DEVIATIONS BETWEEN THE BACKBONE STRUCTURE OF THIS STRUCTURE AND THAT OF THE STRUCTURE IN P6322 (REFERENCE 3).

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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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlblLAP1drop
210 mML-leucinephosphonic acid1drop
30.050 mM1dropZnSO4
4200 mM1dropNaCl
550 mMTris-HCl1drop
650 mMTris-HCl1reservoir
70.050 mM1reservoirZnSO4
8MPD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Dec 8, 1994
RadiationMonochromator: SUPPER DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→36 Å / Num. obs: 144211 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.074
Reflection
*PLUS
Num. measured all: 766198 / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.65→7 Å / σ(F): 2
Details: ALL WATER MOLECULES EXCEPT OF 4 HAVE BEEN REFINED WITH THE PARAM19.SOL PARAMETER FILE IN X-PLOR 3.1. THE FOUR ACTIVE SITE WATER MOLECULES 967, 968, 969, AND 970 HAVE BEEN REFINED TURNING OFF ...Details: ALL WATER MOLECULES EXCEPT OF 4 HAVE BEEN REFINED WITH THE PARAM19.SOL PARAMETER FILE IN X-PLOR 3.1. THE FOUR ACTIVE SITE WATER MOLECULES 967, 968, 969, AND 970 HAVE BEEN REFINED TURNING OFF NON-BONDED INTERACTIONS WITH EACH OTHER IN ORDER TO GET A NON-BIASED VALUE OF THE SHORT DISTANCE BETWEEN WATER MOLECULES 967 AND 968 (2.3 ANG) AND BETWEEN 969 AND 970 (2.1 ANG).
RfactorNum. reflection% reflection
Rfree0.191 --
Rwork0.16 --
obs0.16 112815 81.6 %
Displacement parametersBiso mean: 12.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.65→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 74 968 8440
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_deg21.8
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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