5lhd

Structure of glycosylated human aminopeptidase N

Method: X-RAY DIFFRACTION D_max: 173.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aminopeptidase N

Homo sapiens

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 6 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 36–967	Not recorded	;beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
2	Other combination Monomer Protein × 1 其他Polymer 7 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 36–967	Not recorded	;beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
3	Other combination Monomer Protein × 1 其他Polymer 8 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 36–967	Not recorded	;beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214
4	Other combination Monomer Protein × 1 其他Polymer 8 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 36–967	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；50 mM Imidazol-HCl pH 8.0, 20% PEG6000	Resolution 2.60 Å R-free 0.214

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 5LHD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FYQ Human aminopeptidase N (CD13) Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ZN ZINC ION × 2 SO4 SULFATE ION × 22 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.90 Å R-free 0.193
4FYR Human aminopeptidase N (CD13) in complex with bestatin Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 ZN ZINC ION × 2 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 2 SO4 SULFATE ION × 20 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.91 Å R-free 0.190
4FYS Human aminopeptidase N (CD13) in complex with angiotensin IV Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 2.01 Å R-free 0.198
4FYT Human aminopeptidase N (CD13) in complex with amastatin Deposited 2012-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 66–967（902 aa） Fragment：UNP residues 66-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 2 SO4 SULFATE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop vapor diffusion；pH 5；295 K；2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K	Resolution 1.85 Å R-free 0.183
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6ATK Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N Deposited 2017-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 66–967（902 aa） Fragment：UNP residues 68-967	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% PEG 8000, 1mM GSSG, 1mM GSH, 5% Glycerol, 100mM MES, 1ug/mL endo-beta-N-acetylglucosaminidase A	Resolution 3.50 Å R-free 0.267
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 3.00 Å R-free 0.244
6U7E HCoV-229E RBD Class III in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 3.00 Å R-free 0.244
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.75 Å R-free 0.225
6U7F HCoV-229E RBD Class IV in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.75 Å R-free 0.225
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.35 Å R-free 0.218
6U7G HCoV-229E RBD Class V in complex with human APN Deposited 2019-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 66–967（902 aa） Fragment：ectodomain (UNP residues 66-967)	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5	Resolution 2.35 Å R-free 0.218
7AEW 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and non-canonical binding motifs Deposited 2020-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain BBB 36–73（38 aa） Chain CCC 36–73（38 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.7 0.19 M CaCl2 5% glycerol 27 % PEG400	Resolution 1.20 Å R-free 0.184
7VPQ 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 62–963（902 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
7VPQ 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 62–963（902 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
7VPQ 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 62–963（902 aa）	Not recorded	ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride	Resolution 3.10 Å R-free 0.278
8WDE CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map) Deposited 2023-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 66–967（902 aa） Chain E 66–967（902 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9CAM Aminopeptidase N close state Deposited 2024-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–967（967 aa） Chain B 1–967（967 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9CAO Aminopeptidase N open state Deposited 2024-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–967（967 aa） Chain B 1–967（967 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

13 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–950； UniProt 36–967 Author chain B； PDBConstruct 19–950； UniProt 36–967 Author chain C； PDBConstruct 19–950； UniProt 36–967 Author chain D； PDBConstruct 19–950； UniProt 36–967

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lhd
Deposition date deposition_date	2016-07-11
Structure title title	Structure of glycosylated human aminopeptidase N
Keywords keywords	Human aminopeptidase N, CD13, metalloprotease, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	55.46 Å
Radius of gyration Rg (electron density) rg_electron	54.83 Å
Forward intensity I(0) i0	2661410000.00
Molecular weight molecular_weight	435050.0 kDa
Excluded volume excluded_volume	544230 Å³
Envelope volume envelope_volume	777560 Å³
Hydration-shell volume shell_volume	114190 Å³
Envelope diameter envelope_diameter	164.2 Å
Shell Rg shell_rg	61.09 Å
Envelope Rg envelope_rg	53.34 Å
Shape Rg shape_rg	54.82 Å
Total Rg total_rg	55.00 Å
Total atoms total_atoms	30666
Residues n_residues	3616
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	173.3 Å
Rg (real space) rg_real	55.15 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	2.6610e+09
I(0) uncertainty (real space) i0_real_error	4.7460e+07
Rg (reciprocal space) rg_reciprocal	55.70 Å
I(0) (reciprocal space) i0_reciprocal	2663000000.0000
Solution quality estimate total_estimate	0.8920
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.5 Å
Skewness Skewness skewness	-0.008
Kurtosis Kurtosis kurtosis	-0.710
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	516400000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.858

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Aminopeptidase N
Molecular weight formula_weight	107963.7 kDa
EC 编号 ec_number	3.4.11.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	31338

YPYDVPDYAGAQPARSPGEKNKNANSSPVASTTPSASATTNPASATTLDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTENSK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 branched

Description description	;beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	12

Entity 5 Entity 5 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	6

Entity 6 Entity 6 branched

Description description	;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 8 Entity 8 branched

Description description	;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 10 Entity 10 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	46

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	665

▼

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d5lhda1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.0 — automated matches

Domain ID domain_id	d5lhda2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.0 — automated matches

Domain ID domain_id	d5lhda3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.0 — automated matches

Domain ID domain_id	d5lhda4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.0 — automated matches

Domain ID domain_id	d5lhdb1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.0 — automated matches

Domain ID domain_id	d5lhdb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.0 — automated matches

Domain ID domain_id	d5lhdb3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.0 — automated matches

Domain ID domain_id	d5lhdb4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.0 — automated matches

Domain ID domain_id	d5lhdc1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.0 — automated matches

Domain ID domain_id	d5lhdc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.0 — automated matches

Domain ID domain_id	d5lhdc3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.0 — automated matches

Domain ID domain_id	d5lhdc4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.0 — automated matches

Domain ID domain_id	d5lhdd1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.0 — automated matches

Domain ID domain_id	d5lhdd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.0 — automated matches

Domain ID domain_id	d5lhdd3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.0 — automated matches

Domain ID domain_id	d5lhdd4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	5lhdA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	5lhdA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	5lhdA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

Domain ID domain_id	5lhdA04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	50 — Zincin-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5lhdB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	5lhdB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	5lhdB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

Domain ID domain_id	5lhdB04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	50 — Zincin-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5lhdC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	5lhdC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	5lhdC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

Domain ID domain_id	5lhdC04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	50 — Zincin-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5lhdD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	5lhdD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	5lhdD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

Domain ID domain_id	5lhdD04
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	50 — Zincin-like fold
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	127.093 Å
Unit-cell length b length_b	168.856 Å
Unit-cell length c length_c	244.249 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.973 Å
R factor r_factor	0.1831
R_work r_work	0.1815
R_free r_free	0.2141