SAXSdb — 2wqz

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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 43–619	Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	NEUREXIN-1-BETA × 1 （Q63373） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 43–619	Fragment：ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	NEUREXIN-1-BETA × 1 （Q63373） 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

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 2WQZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 44–619（576 aa） Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	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
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 44–619（576 aa） Fragment：CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619	Not recorded	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
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 12–588； UniProt 43–619 Author chain B； PDBConstruct 12–588； UniProt 43–619

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 D； UniProt 80–200 Chain D； UniProt 201–258	Fragment：LNS DOMAIN, RESIDUES 80-258	NEUROLIGIN 4, X-LINKED × 1 （Q8N0W4） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 80–200 Chain C； UniProt 201–258	Fragment：LNS DOMAIN, RESIDUES 80-258	NEUROLIGIN 4, X-LINKED × 1 （Q8N0W4） 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

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 2WQZ	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	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 C 80–258（179 aa） Fragment：LNS DOMAIN, RESIDUES 80-258	Not recorded	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
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	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 D 80–258（179 aa） Fragment：LNS DOMAIN, RESIDUES 80-258	Not recorded	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
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 1–121； UniProt 80–200 Author chain C； PDBConstruct 122–179； UniProt 201–258 Author chain D； PDBConstruct 1–121； UniProt 80–200 Author chain D； PDBConstruct 122–179； UniProt 201–258

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	2wqz
Deposition date deposition_date	2009-08-28
Structure title title	Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement
Keywords keywords	;TRANSMEMBRANE, DISULFIDE BOND, ALPHA/BETA-HYDROLASE CHOLINESTERASE AUTISM BRAIN, ALTERNATIVE PROMOTER USAGE, MEMBRANE, GLYCOPROTEIN, 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	43.01 Å
Radius of gyration Rg (electron density) rg_electron	42.85 Å
Forward intensity I(0) i0	381132000.00
Molecular weight molecular_weight	160930.0 kDa
Excluded volume excluded_volume	201300 Å³
Envelope volume envelope_volume	270630 Å³
Hydration-shell volume shell_volume	53906 Å³
Envelope diameter envelope_diameter	143.8 Å
Shell Rg shell_rg	46.46 Å
Envelope Rg envelope_rg	42.43 Å
Shape Rg shape_rg	42.81 Å
Total Rg total_rg	43.17 Å
Total atoms total_atoms	11360
Residues n_residues	1443
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	138.8 Å
Rg (real space) rg_real	43.12 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	3.8110e+08
I(0) uncertainty (real space) i0_real_error	7.1090e+06
Rg (reciprocal space) rg_reciprocal	43.01 Å
I(0) (reciprocal space) i0_reciprocal	381100000.0000
Solution quality estimate total_estimate	0.8678
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.2 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-0.652
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45740000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.571

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	11360

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	NORWAY 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	2

Entity 4 Entity 4 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) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2wqzc_
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	d2wqzd_
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	2wqzA00
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	2wqzB00
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	2wqzC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2wqzD00
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	158.520 Å
Unit-cell length b length_b	198.670 Å
Unit-cell length c length_c	85.740 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	3.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2080
R_work r_work	0.2050
R_free r_free	0.2760

fit	/app/data/saxs_computation/wq/2wqz/2wqz.fit
pddf	/app/data/pr_computation/wq/2wqz/2wqz.pr.out
profile	/app/data/saxs_computation/wq/2wqz/2wqz.dat

Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement

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 (4)

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

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)