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5z65

Crystal structure of porcine aminopeptidase N ectodomain in functional form

Method: X-RAY DIFFRACTION Dmax: 97.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aminopeptidase

Sus scrofa

UniProt K7GMF9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 8 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 63–963 Fragment：N ectodomain ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；100 mM Hepes pH 7.2, 0.2 M sodium fluoride, 25% PEG 3350 Resolution 2.65 Å R-free 0.251

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 5Z65 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7VPP Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans Deposited 2021-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 58–961（904 aa）
Chain C 58–961（904 aa）
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 8% w/v Polyethylene glycol 1000, 8% w/v Polyethylene glycol 8000 and 20% w/v Glycerol
Resolution 2.69 Å R-free 0.230

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K7GMF9_PIG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–903； UniProt 63–963

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 5z65

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5z65
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5z65
Deposition date deposition_date2018-01-22
Structure title titleCrystal structure of porcine aminopeptidase N ectodomain in functional form
Keywords keywordsHYDROLASE; 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_guinier31.08 Å
Radius of gyration Rg (electron density) rg_electron30.02 Å
Forward intensity I(0) i0177164000.00
Molecular weight molecular_weight106310.0 kDa
Excluded volume excluded_volume133050 ų
Envelope volume envelope_volume169240 ų
Hydration-shell volume shell_volume45506 ų
Envelope diameter envelope_diameter98.2 Å
Shell Rg shell_rg38.53 Å
Envelope Rg envelope_rg29.77 Å
Shape Rg shape_rg30.00 Å
Total Rg total_rg30.85 Å
Total atoms total_atoms7495
Residues n_residues900
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 dmax97.1 Å
Rg (real space) rg_real30.92 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real1.7720e+08
I(0) uncertainty (real space) i0_real_error2.8740e+06
Rg (reciprocal space) rg_reciprocal30.99 Å
I(0) (reciprocal space) i0_reciprocal177200000.0000
Solution quality estimate total_estimate0.9004
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.0 Å
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52180000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5z65a1
Class classb — All beta proteins
Fold Fold foldb.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamilyb.98.1 — Zn aminopeptidase N-terminal domain
Family Family familyb.98.1.0 — automated matches
Domain ID domain_idd5z65a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.0 — automated matches
Domain ID domain_idd5z65a3
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.30 — Zn aminopeptidase insert domain
Family Family familyb.1.30.0 — automated matches
Domain ID domain_idd5z65a4
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id5z65A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1730 — tricorn interacting facor f3 domain
Domain ID domain_id5z65A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily10 — Neutral Protease Domain 2
Domain ID domain_id5z65A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1910 —
Domain ID domain_id5z65A04
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology50 — Zincin-like fold
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)