SAXSdb — 3vkf

▼

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

Neuroligin-1

Rattus norvegicus

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 Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 45–638 Chain B； UniProt 45–638	Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Neurexin-1-beta × 2 （Q28142） 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 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 45–638	Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	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	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 45–638	Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287

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 3VKF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BIW Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex Deposited 2007-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain A 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain A 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain D 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1	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 6；293 K；8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.276
3BIW Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex Deposited 2007-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain B 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain B 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 46–164（119 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 185–297（113 aa） Fragment：extracellular esterase domain of Neuroligin-1 Chain C 306–638（333 aa） Fragment：extracellular esterase domain of Neuroligin-1	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.276
3BIX Crystal structure of the extracellular esterase domain of Neuroligin-1 Deposited 2007-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 46–164（119 aa） Fragment：extracellular esterase domain Chain A 185–297（113 aa） Fragment：extracellular esterase domain Chain A 306–638（333 aa） Fragment：extracellular esterase domain Chain C 46–164（119 aa） Fragment：extracellular esterase domain Chain C 185–297（113 aa） Fragment：extracellular esterase domain Chain C 306–638（333 aa） Fragment：extracellular esterase domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；1.2 M tri-Sodium citrate, 0.1 M Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.205
3BIX Crystal structure of the extracellular esterase domain of Neuroligin-1 Deposited 2007-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 46–164（119 aa） Fragment：extracellular esterase domain Chain B 185–297（113 aa） Fragment：extracellular esterase domain Chain B 306–638（333 aa） Fragment：extracellular esterase domain Chain D 46–164（119 aa） Fragment：extracellular esterase domain Chain D 185–297（113 aa） Fragment：extracellular esterase domain Chain D 306–638（333 aa） Fragment：extracellular esterase domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；1.2 M tri-Sodium citrate, 0.1 M Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.205

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLGN1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–585； UniProt 45–638 Author chain B； PDBConstruct 1–585； UniProt 45–638

Neurexin-1-beta

Bos taurus

UniProt Q28142

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 Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 83–290 Chain D； UniProt 83–290	Fragment：LNS domain (UNP RESIDUES 83-290)	Neuroligin-1 × 2 （Q62765） 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 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 83–290	Fragment：LNS domain (UNP RESIDUES 83-290)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 83–290	Fragment：LNS domain (UNP RESIDUES 83-290)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.287

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	NRX1B_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–180； UniProt 83–290 Author chain D； PDBConstruct 3–180； UniProt 83–290

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3vkf
Deposition date deposition_date	2011-11-15
Structure title title	Crystal Structure of Neurexin 1beta/Neuroligin 1 complex
Keywords keywords	Alpha/Beta Hydrolase, Beta-sandwich, Synapse Matulation, Calcium Binding, N-glycosylation, Membrane, Cell Adhesion; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.51 Å
Radius of gyration Rg (electron density) rg_electron	42.46 Å
Forward intensity I(0) i0	371050000.00
Molecular weight molecular_weight	160240.0 kDa
Excluded volume excluded_volume	201090 Å³
Envelope volume envelope_volume	266480 Å³
Hydration-shell volume shell_volume	53466 Å³
Envelope diameter envelope_diameter	146.3 Å
Shell Rg shell_rg	46.27 Å
Envelope Rg envelope_rg	42.26 Å
Shape Rg shape_rg	42.41 Å
Total Rg total_rg	42.83 Å
Total atoms total_atoms	11320
Residues n_residues	1441
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

▼

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

Maximum dimension Dmax dmax	144.5 Å
Rg (real space) rg_real	42.63 Å
Rg uncertainty (real space) rg_real_error	1.62 Å
I(0) (real space) i0_real	3.7110e+08
I(0) uncertainty (real space) i0_real_error	7.2020e+06
Rg (reciprocal space) rg_reciprocal	42.51 Å
I(0) (reciprocal space) i0_reciprocal	371000000.0000
Solution quality estimate total_estimate	0.8725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42240000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.839

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Neuroligin-1
Molecular weight formula_weight	65351.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11320

SQKLDDVDPLVTTNFGKIRGIKKELNNEILGPVIQFLGVPYAAPPTGEHRFQPPEPPSPWSDIRNATQFAPVCPQNIIDGRLPEVMLPVWFTNNLDVVSSYVQDQSEDCLYLNIYVPTEDVKRISKECARKPGKKICRKGDIRDSGGPKPVMVYIHGGSYMEGTGNLYDGSVLASYGNVIVITVNYRLGVLGFLSTGDQAAKGNYGLLDLIQALRWTSENIGFFGGDPLRITVFGSGAGGSCVNLLTLSHYSEGLFQRAIAQSGTALSSWAVSFQPAKYARILATKVGCNVSDTVELVECLQKKPYKELVDQDVQPARYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVENIVDSDDGVSASDFDFAVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRHNPETRRKTLLALFTDHQWVAPAVATADLHSNFGSPTYFYAFYHHCQTDQVPAWADAAHGDEVPYVLGIPMIGPTELFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWTRYSQKDQLYLHIGLKPRVKEHYRANKVNLWLELVPHLHNLND

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Neurexin-1-beta
Molecular weight formula_weight	19560.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSGTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVS

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 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	1

Entity 4 Entity 4 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	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3vkfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3vkfB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3vkfC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3vkfD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	81.261 Å
Unit-cell length b length_b	95.186 Å
Unit-cell length c length_c	120.396 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.910 Å
R factor r_factor	0.2137
R_work r_work	0.2052
R_free r_free	0.2869

fit	/app/data/saxs_computation/vk/3vkf/3vkf.fit
pddf	/app/data/pr_computation/vk/3vkf/3vkf.pr.out
profile	/app/data/saxs_computation/vk/3vkf/3vkf.dat

Crystal Structure of Neurexin 1beta/Neuroligin 1 complex

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

Neuroligin-1

State in the Current Structure

Other States of the Same Protein in the Database

Neurexin-1-beta

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)