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2ewb

The crystal structure of Bovine Lens Leucine Aminopeptidase in complex with zofenoprilat

Method: X-RAY DIFFRACTION Dmax: 83.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytosol aminopeptidase

OrganismNot specified

UniProt P00727

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–486 Not recorded ZN ZINC ION × 12 NA SODIUM ION × 6 CO3 CARBONATE ION × 6 ZED L-PROLINE, 1-[(2S)-3-MERCAPTO-2-METHYL-1-OXOPROPYL]-4-(PHENYLTHIO)-, 4S × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 24 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；TRIS/HCl pH 7.8, MPD, Zinc chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298. Resolution 1.85 Å R-free 0.177

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2EWB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BLL 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 Deposited 1993-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–487（487 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
1BPM DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY Deposited 1993-03-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–487（487 aa）
Not recorded MG MAGNESIUM ION × 6 ZN ZINC ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1BPN DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY Deposited 1993-03-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–487（487 aa）
Not recorded ZN ZINC ION × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å
1LAM LEUCINE AMINOPEPTIDASE (UNLIGATED) Deposited 1995-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–484（484 aa）
Not recorded ZN ZINC ION × 18 CO3 CARBONATE ION × 6 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 1.60 Å R-free 0.204
1LAN LEUCINE AMINOPEPTIDASE COMPLEX WITH L-LEUCINAL Deposited 1995-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–484（484 aa）
Not recorded ZN ZINC ION × 18 LEU LEUCINE × 6 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 18 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；pH 7.8
Resolution 1.90 Å R-free 0.212
1LAP MOLECULAR STRUCTURE OF LEUCINE AMINOPEPTIDASE AT 2.7-ANGSTROMS RESOLUTION Deposited 1990-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–487（487 aa）
Not recorded ZN ZINC ION × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1LCP BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE PHOSPHONIC ACID Deposited 1995-05-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–484（484 aa）
Chain B 1–484（484 aa）
Not recorded ZN ZINC ION × 18 PLU LEUCINE PHOSPHONIC ACID × 6 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 18 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.65 Å R-free 0.191
2J9A blLAP in Complex with Microginin FR1 Deposited 2006-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–487（487 aa）
Not recorded CL CHLORIDE ION × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 18 DMS DIMETHYL SULFOXIDE × 12 ZN ZINC ION × 12 AHY (2S,3R)-3-AMINO-2-HYDROXYDECANOIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；HANGING DROP BLLAP 7MG/ML IN 50MM TRIS-HCL PH7.8, 50UM ZNSO4, 200MM NACL EQUILIBRATED AGAINST 50MM TRIS-HCL PH7.8, 50UM ZNSO4, 200MM NACL, 50% MPD, pH 7.80
Resolution 1.73 Å R-free 0.173

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMPL_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–486； UniProt 1–486

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2ewb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ewb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ewb
Deposition date deposition_date2005-11-02
Structure title titleThe crystal structure of Bovine Lens Leucine Aminopeptidase in complex with zofenoprilat
Keywords keywordsAMINOPEPTIDASE, METALLOPEPTIDASE, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.49 Å
Radius of gyration Rg (electron density) rg_electron23.82 Å
Forward intensity I(0) i047483300.00
Molecular weight molecular_weight53796.0 kDa
Excluded volume excluded_volume67405 ų
Envelope volume envelope_volume76925 ų
Hydration-shell volume shell_volume27150 ų
Envelope diameter envelope_diameter87.0 Å
Shell Rg shell_rg30.86 Å
Envelope Rg envelope_rg24.35 Å
Shape Rg shape_rg23.83 Å
Total Rg total_rg24.52 Å
Total atoms total_atoms3772
Residues n_residues486
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.5 Å
Rg (real space) rg_real24.57 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real4.7480e+07
I(0) uncertainty (real space) i0_real_error6.6530e+05
Rg (reciprocal space) rg_reciprocal24.55 Å
I(0) (reciprocal space) i0_reciprocal47480000.0000
Solution quality estimate total_estimate0.8629
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5 Å
Skewness Skewness skewness0.489
Kurtosis Kurtosis kurtosis-0.142
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13310000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2ewba1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamilyc.56.5 — Zn-dependent exopeptidases
Family Family familyc.56.5.3 — Leucine aminopeptidase, C-terminal domain
Domain ID domain_idd2ewba2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2ewbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id2ewbA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
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8. Citations (1)

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9. Files and Curves (10)