SAXSdb — 3biw

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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 46–164 Chain A； UniProt 185–297 Chain A； UniProt 306–638 Chain D； UniProt 46–164 Chain D； UniProt 185–297 Chain D； UniProt 306–638	Fragment：extracellular esterase domain of Neuroligin-1	Neurexin-1-beta × 2 （Q63373） 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 × 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
2	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 46–164 Chain B； UniProt 185–297 Chain B； UniProt 306–638 Chain C； UniProt 46–164 Chain C； UniProt 185–297 Chain C； UniProt 306–638	Fragment：extracellular esterase domain of Neuroligin-1	Neurexin-1-beta × 2 （Q63373） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 3BIW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BIX Crystal structure of the extracellular esterase domain of Neuroligin-1 Deposited 2007-12-01	Different construct 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 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
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	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 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638) Chain B 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	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
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	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
3VKF Crystal Structure of Neurexin 1beta/Neuroligin 1 complex Deposited 2011-11-15	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 B 45–638（594 aa） Fragment：Acetylcholinesterase-like domain (UNP RESIDUES 45-638)	Not recorded	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

2 other PDB entries and 5 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 4–122； UniProt 46–164 Author chain A； PDBConstruct 123–235； UniProt 185–297 Author chain A； PDBConstruct 236–568； UniProt 306–638 Author chain B； PDBConstruct 4–122； UniProt 46–164 Author chain B； PDBConstruct 123–235； UniProt 185–297 Author chain B； PDBConstruct 236–568； UniProt 306–638 Author chain C； PDBConstruct 4–122； UniProt 46–164 Author chain C； PDBConstruct 123–235； UniProt 185–297 Author chain C； PDBConstruct 236–568； UniProt 306–638 Author chain D； PDBConstruct 4–122； UniProt 46–164 Author chain D； PDBConstruct 123–235； UniProt 185–297 Author chain D； PDBConstruct 236–568； UniProt 306–638

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	Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 47–201 Chain E； UniProt 232–299 Chain H； UniProt 47–201 Chain H； UniProt 232–299	Fragment：extracellular LNS domain of Neurexin-1beta	Neuroligin-1 × 2 （Q62765） 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 × 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
2	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 47–201 Chain F； UniProt 232–299 Chain G； UniProt 47–201 Chain G； UniProt 232–299	Fragment：extracellular LNS domain of Neurexin-1beta	Neuroligin-1 × 2 （Q62765） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 3BIW	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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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
2XB6 Revisited crystal structure of Neurexin1beta-Neuroligin4 complex Deposited 2010-04-07	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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

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 E； PDBConstruct 15–169； UniProt 47–201 Author chain E； PDBConstruct 170–237； UniProt 232–299 Author chain F； PDBConstruct 15–169； UniProt 47–201 Author chain F； PDBConstruct 170–237； UniProt 232–299 Author chain G； PDBConstruct 15–169； UniProt 47–201 Author chain G； PDBConstruct 170–237； UniProt 232–299 Author chain H； PDBConstruct 15–169； UniProt 47–201 Author chain H； PDBConstruct 170–237； UniProt 232–299

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	3biw
Deposition date deposition_date	2007-12-01
Structure title title	Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex
Keywords keywords	;protein-protein complex, esterase domain, LNS domain, alpha-beta hydrolase, Cell adhesion, Cell junction, Glycoprotein, Membrane, Postsynaptic cell membrane, Synapse, Transmembrane, Alternative promoter usage, Cell adhesion-Cell adhesion COMPLEX ;; 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	48.43 Å
Radius of gyration Rg (electron density) rg_electron	48.00 Å
Forward intensity I(0) i0	1416890000.00
Molecular weight molecular_weight	317600.0 kDa
Excluded volume excluded_volume	398630 Å³
Envelope volume envelope_volume	538470 Å³
Hydration-shell volume shell_volume	91976 Å³
Envelope diameter envelope_diameter	173.1 Å
Shell Rg shell_rg	53.73 Å
Envelope Rg envelope_rg	46.95 Å
Shape Rg shape_rg	47.96 Å
Total Rg total_rg	48.33 Å
Total atoms total_atoms	22438
Residues n_residues	2840
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	160.9 Å
Rg (real space) rg_real	48.13 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	1.4170e+09
I(0) uncertainty (real space) i0_real_error	2.5290e+07
Rg (reciprocal space) rg_reciprocal	48.43 Å
I(0) (reciprocal space) i0_reciprocal	1417000000.0000
Solution quality estimate total_estimate	0.8845
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.4 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	110600000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Neuroligin-1
Molecular weight formula_weight	64229.0 kDa
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	22438

ADPQKLDDVDPLVTTNFGKIRGIKKELNNEILGPVIQFLGVPYAAPPTGEHRFQPPEPPSPWSDIRNATQFAPVCPQNIIDGRLPEVMLPVWFTNNLDVVSSYVQDQSEDCLYLNIYVPTEDDIRDSGGPKPVMVYIHGGSYMEGTGNLYDGSVLASYGNVIVITVNYRLGVLGFLSTGDQAAKGNYGLLDLIQALRWTSENIGFFGGDPLRITVFGSGAGGSCVNLLTLSHYSEKGLFQRAIAQSGTALSSWAVSFQPAKYARILATKVGCNVSDTVELVECLQKKPYKELVDQDVQPARYHIAFGPVIDGDVIPDDPQILMEQGEFLNYDIMLGVNQGEGLKFVENIVDSDDGVSASDFDFAVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRHNPETRRKTLLALFTDHQWVAPAVATADLHSNFGSPTYFYAFYHHCQTDQVPAWADAAHGDEVPYVLGIPMIGPTELFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVAWTRYSQKDQLYLHIGLKPRVKEHYRANKVNLWLELVPHLHNLNDHHHHHH

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Neurexin-1-beta
Molecular weight formula_weight	26030.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GSPGISGGGGGILEASSLGAHHIHHFHGSSKHHSVPIAIYRSPASLRGGHAGTTYIFSKGGGQITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPSSMTTESHHHHHH

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	Trichoplusia ni

Entity 3 Entity 3 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	3

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	12

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	6

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3biwe1
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	d3biwf1
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	d3biwg1
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	d3biwh1
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 (8 domains)

Domain ID domain_id	3biwA00
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	3biwB00
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	3biwC00
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	3biwD00
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	3biwE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3biwF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3biwG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3biwH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	229.830 Å
Unit-cell length b length_b	148.796 Å
Unit-cell length c length_c	123.602 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	45.900 Å
R factor r_factor	—
R_work r_work	0.2460
R_free r_free	0.2760

fit	/app/data/saxs_computation/bi/3biw/3biw.fit
pddf	/app/data/pr_computation/bi/3biw/3biw.pr.out
profile	/app/data/saxs_computation/bi/3biw/3biw.dat

Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion 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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)