SAXSdb — 2xb6

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

NEUROLIGIN-4, X-LINKED

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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 44–619	Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	NEUREXIN-1-BETA × 1 （Q63373） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 44–619	Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	NEUREXIN-1-BETA × 1 （Q63373） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 14 CL CHLORIDE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236

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 2XB6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 43–619（577 aa） Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 Å R-free 0.276
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 43–619（577 aa） Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 Å R-free 0.276
3BE8 Crystal structure of the synaptic protein neuroligin 4 Deposited 2007-11-16	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 44–619（576 aa） Fragment：extracellular cholinesterase-like domain Chain B 44–619（576 aa） Fragment：extracellular cholinesterase-like domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FLC CITRATE ANION × 2 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 6 NA SODIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；10% PEG-3000, 0.1M sodium phosphate-citrate, 0.3M sodium chloride, 0.01M calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.201

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLGNX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–588； UniProt 44–619 Author chain B； PDBConstruct 13–588； UniProt 44–619

NEUREXIN-1-BETA

RATTUS NORVEGICUS

UniProt Q63373

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 80–258	Fragment：LNS DOMAIN, RESIDUES 80-258	NEUROLIGIN-4, X-LINKED × 1 （Q8N0W4） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 80–258	Fragment：LNS DOMAIN, RESIDUES 80-258	NEUROLIGIN-4, X-LINKED × 1 （Q8N0W4） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 14 CL CHLORIDE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；100MM MES PH6.3,10% PEG 20000, 2MM CACL2	Resolution 2.60 Å R-free 0.236

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 2XB6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
1C4R THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING Deposited 1999-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 81–292（212 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.279
2R1B Crystal Structure of rat neurexin 1beta with a splice insert at SS#4 Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 77–294（218 aa） Fragment：LNS/LG domain	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；17% Peg 8000, 0.1 M Tris pH 8.5, 0.2 M MgCl2, 5 mM CaCl2, 0.5% beta-octyl-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.72 Å R-free 0.225
2R1B Crystal Structure of rat neurexin 1beta with a splice insert at SS#4 Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 77–294（218 aa） Fragment：LNS/LG domain	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；17% Peg 8000, 0.1 M Tris pH 8.5, 0.2 M MgCl2, 5 mM CaCl2, 0.5% beta-octyl-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.72 Å R-free 0.225
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain W 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2R1D Crystal structure of rat neurexin 1beta in the Ca2+ containing form Deposited 2007-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 78–302（225 aa） Fragment：LNS/LG domain	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.60 Å R-free 0.244
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 80–200（121 aa） Fragment：LNS DOMAIN, RESIDUES 80-258 Chain D 201–258（58 aa） Fragment：LNS DOMAIN, RESIDUES 80-258	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 Å R-free 0.276
2WQZ Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement Deposited 2009-08-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 80–200（121 aa） Fragment：LNS DOMAIN, RESIDUES 80-258 Chain C 201–258（58 aa） Fragment：LNS DOMAIN, RESIDUES 80-258	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 0.1M MES PH6.5	Resolution 3.90 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 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 47–201（155 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain E 232–299（68 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain H 47–201（155 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain H 232–299（68 aa） Fragment：extracellular LNS domain of Neurexin-1beta	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 F 47–201（155 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain F 232–299（68 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain G 47–201（155 aa） Fragment：extracellular LNS domain of Neurexin-1beta Chain G 232–299（68 aa） Fragment：extracellular LNS domain of Neurexin-1beta	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

5 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRX1B_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–179； UniProt 80–258 Author chain D； PDBConstruct 1–179； UniProt 80–258

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	2xb6
Deposition date deposition_date	2010-04-07
Structure title title	Revisited crystal structure of Neurexin1beta-Neuroligin4 complex
Keywords keywords	ALPHA-BETA-HYDROLASE FOLD, AUTISM, CONFORMATIONAL REARRANGEMENT, CELL ADHESION; CELL ADHESION
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	42.76 Å
Radius of gyration Rg (electron density) rg_electron	42.62 Å
Forward intensity I(0) i0	380302000.00
Molecular weight molecular_weight	161390.0 kDa
Excluded volume excluded_volume	202140 Å³
Envelope volume envelope_volume	263570 Å³
Hydration-shell volume shell_volume	52870 Å³
Envelope diameter envelope_diameter	151.2 Å
Shell Rg shell_rg	46.33 Å
Envelope Rg envelope_rg	42.29 Å
Shape Rg shape_rg	42.57 Å
Total Rg total_rg	42.94 Å
Total atoms total_atoms	11371
Residues n_residues	1423
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	143.3 Å
Rg (real space) rg_real	42.88 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	3.8030e+08
I(0) uncertainty (real space) i0_real_error	7.2360e+06
Rg (reciprocal space) rg_reciprocal	42.76 Å
I(0) (reciprocal space) i0_reciprocal	380200000.0000
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	42.6 Å
Skewness Skewness skewness	0.329
Kurtosis Kurtosis kurtosis	-0.632
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42320000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.781

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	NEUROLIGIN-4, X-LINKED
Molecular weight formula_weight	66230.2 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	11720

DYKDDDDKLAAAQYPVVNTNYGKIRGLRTPLPNEILGPVEQYLGVPYASPPTGERRFQPPEPPSSWTGIRNTTQFAAVCPQHLDERSLLHDMLPIWFTANLDTLMTYVQDQNEDCLYLNIYVPTEDDIHDQNSKKPVMVYIHGGSYMEGTGNMIDGSILASYGNVIVITINYRLGILGFLSTGDQAAKGNYGLLDQIQALRWIEENVGAFGGDPKRVTIFGSGAGASCVSLLTLSHYSEGLFQKAIIQSGTALSSWAVNYQPAKYTRILADKVGCNMLDTTDMVECLRNKNYKELIQQTITPATYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVDGIVDNEDGVTPNDFDFSVSNFVDNLYGYPEGKDTLRETIKFMYTDWADKENPETRRKTLVALFTDHQWVAPAVATADLHAQYGSPTYFYAFYHHCQSEMKPSWADSAHGDEVPYVFGIPMIGPTELFSCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWSRYNPKDQLYLHIGLKPRVRDHYRATKVAFWLELVPHLHNLNEIFQYVSTTTKVPPPDMT

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	HOMO SAPIENS

Entity 2 Entity 2 polymer

Description description	NEUREXIN-1-BETA
Molecular weight formula_weight	19367.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GGHAGTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLV

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	ESCHERICHIA COLI BL21(DE3)

Entity 3 Entity 3 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	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2xb6a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d2xb6a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2xb6b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d2xb6b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2xb6c_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.4 — Laminin G-like module

Domain ID domain_id	d2xb6d_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.4 — Laminin G-like module

CATH v4.4 (4 domains)

Domain ID domain_id	2xb6A00
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	2xb6B00
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	2xb6C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2xb6D00
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	136.307 Å
Unit-cell length b length_b	198.779 Å
Unit-cell length c length_c	85.896 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2050
R_work r_work	0.2040
R_free r_free	0.2360

fit	/app/data/saxs_computation/xb/2xb6/2xb6.fit
pddf	/app/data/pr_computation/xb/2xb6/2xb6.pr.out
profile	/app/data/saxs_computation/xb/2xb6/2xb6.dat

Revisited crystal structure of Neurexin1beta-Neuroligin4 complex

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

NEUROLIGIN-4, X-LINKED

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)