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1bpm

DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY

Method: X-RAY DIFFRACTION Dmax: 84.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LEUCINE AMINOPEPTIDASE

Bos taurus

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 1–487 Not recorded MG MAGNESIUM ION × 6 ZN ZINC ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å

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 1BPM 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 mutation/modification Different oligomeric state Different ligand/ion 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
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 ligand/ion 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 ligand/ion 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 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
2EWB The crystal structure of Bovine Lens Leucine Aminopeptidase in complex with zofenoprilat Deposited 2005-11-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–486（486 aa）
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
2J9A blLAP in Complex with Microginin FR1 Deposited 2006-11-06 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 1–487； UniProt 1–487

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 1bpm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bpm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bpm
Deposition date deposition_date1993-03-02
Structure title titleDIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY
Keywords keywordsHYDROLASE(ALPHA-AMINOACYLPEPTIDE); HYDROLASE(ALPHA-AMINOACYLPEPTIDE)
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_guinier24.44 Å
Radius of gyration Rg (electron density) rg_electron23.80 Å
Forward intensity I(0) i045312100.00
Molecular weight molecular_weight52287.0 kDa
Excluded volume excluded_volume65452 ų
Envelope volume envelope_volume74451 ų
Hydration-shell volume shell_volume26544 ų
Envelope diameter envelope_diameter87.8 Å
Shell Rg shell_rg30.59 Å
Envelope Rg envelope_rg24.19 Å
Shape Rg shape_rg23.81 Å
Total Rg total_rg24.49 Å
Total atoms total_atoms3673
Residues n_residues481
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 dmax84.2 Å
Rg (real space) rg_real24.52 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real4.5310e+07
I(0) uncertainty (real space) i0_real_error7.0980e+05
Rg (reciprocal space) rg_reciprocal24.50 Å
I(0) (reciprocal space) i0_reciprocal45310000.0000
Solution quality estimate total_estimate0.8555
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.7 Å
Skewness Skewness skewness0.497
Kurtosis Kurtosis kurtosis-0.110
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11390000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.916; Smooth: 0.982
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bpma1
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_idd1bpma2
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.50.1.1 — Leucine aminopeptidase (Aminopeptidase A), N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id1bpmA01
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_id1bpmA02
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 (3)

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9. Files and Curves (10)