SAXSdb — 4plm

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

Netrin-1

Gallus gallus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–457	Fragment：LN-LE3 (UNP residues 26-457)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；298 K；NaoAc, NaCacodylate	Resolution 2.80 Å R-free 0.257
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–457	Fragment：LN-LE3 (UNP residues 26-457)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；298 K；NaoAc, NaCacodylate	Resolution 2.80 Å R-free 0.257

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 4PLM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4PLN Crystal Structure of Chicken Netrin-1 (LN-LE3) complexed with mouse Neogenin (FN4-5) Deposited 2014-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457) Chain B 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.1M Hepes pH 7.0, 12% PEG3350	Resolution 3.20 Å R-free 0.239
4PLO Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5) Deposited 2014-05-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–457（432 aa） Fragment：LN-LE3 (UNP residues 26-457)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 SO4 SULFATE ION × 10 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate	Resolution 2.90 Å R-free 0.288
7LER Netrin-1 filament assembly Deposited 2021-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 48 PDB declaration: 48-meric	Chain A 26–458（433 aa） Chain B 26–458（433 aa） Chain C 26–458（433 aa） Chain D 26–458（433 aa） Chain E 26–458（433 aa） Chain F 26–458（433 aa） Chain G 26–458（433 aa） Chain H 26–458（433 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 96	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；40% MPD, 100 mM Tris	Resolution 5.99 Å R-free 0.368
7LRF Netrin-1 in complex with SOS Deposited 2021-02-16	Different construct Different mutation/modification 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 26–458（433 aa） Chain B 26–458（433 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 CA CALCIUM ION × 2 NA SODIUM ION × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293.15 K；20% PEG 8000, 100 mM CHES	Resolution 3.21 Å R-free 0.281
8TSM Crystal structure of chicken Netrin-1 LN LE1-2 Deposited 2023-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–405（380 aa） Fragment：residues 26-405	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350	Resolution 3.90 Å R-free 0.319
9D77 Crystal form of Netrin-1 mimics nanotubes Deposited 2024-08-16	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 26–458（433 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5	Resolution 3.40 Å R-free 0.335

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NET1_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–432； UniProt 26–457

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4plm
Deposition date deposition_date	2014-05-18
Structure title title	Crystal Structure of Chicken Netrin-1 (LN-LE3)
Keywords keywords	elongated, cysteine rich, glycoprotein, PROTEIN BINDING; PROTEIN BINDING
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	35.06 Å
Radius of gyration Rg (electron density) rg_electron	36.07 Å
Forward intensity I(0) i0	42388200.00
Molecular weight molecular_weight	47391.0 kDa
Excluded volume excluded_volume	57673 Å³
Envelope volume envelope_volume	80414 Å³
Hydration-shell volume shell_volume	22456 Å³
Envelope diameter envelope_diameter	141.6 Å
Shell Rg shell_rg	34.14 Å
Envelope Rg envelope_rg	37.55 Å
Shape Rg shape_rg	36.00 Å
Total Rg total_rg	36.11 Å
Total atoms total_atoms	3301
Residues n_residues	416
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	133.4 Å
Rg (real space) rg_real	36.00 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	4.2390e+07
I(0) uncertainty (real space) i0_real_error	7.5610e+05
Rg (reciprocal space) rg_reciprocal	35.41 Å
I(0) (reciprocal space) i0_reciprocal	42370000.0000
Solution quality estimate total_estimate	0.6447
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.822
Kurtosis Kurtosis kurtosis	0.066
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2134000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.290; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.084; Smooth: 0.425

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Netrin-1
Molecular weight formula_weight	48545.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3383

GYPGLNMFAVQTAQPDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIP

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	Chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Baculoviridae

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4plmA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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8. Citations (1)

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Unit-cell length a length_a	62.627 Å
Unit-cell length b length_b	62.627 Å
Unit-cell length c length_c	269.788 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.801 Å
Low-resolution limit resolution_low	28.639 Å
R factor r_factor	0.1989
R_work r_work	0.1923
R_free r_free	0.2571

fit	/app/data/saxs_computation/pl/4plm/4plm.fit
pddf	/app/data/pr_computation/pl/4plm/4plm.pr.out
profile	/app/data/saxs_computation/pl/4plm/4plm.dat

Crystal Structure of Chicken Netrin-1 (LN-LE3)

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

Netrin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction