SAXSdb — 5xeq

▼

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

Neuroligin-2

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	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 42–611	Fragment：UNP residues 42-610 Mutation：N98Q	MAM domain-containing glycosylphosphatidylinositol anchor protein 1 × 2 （Q8NFP4） 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	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；300mM Ammonium citrate tribasic, pH 7.0, 13% 1,3-Butanediol and 18%(v/v) PEG3350	Resolution 3.14 Å R-free 0.278

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 5XEQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8GS4 Cryo-EM structure of human Neuroligin 2 Deposited 2022-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–835（835 aa） Chain B 1–835（835 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9FAJ CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38, in a desensitised state (StateD1) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 668–700（33 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 5 D10 DECANE × 12 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 5 ABU GAMMA-AMINO-BUTANOIC ACID × 2 CL CHLORIDE ION × 4 R16 HEXADECANE × 4 HEX HEXANE × 7 PLM PALMITIC ACID × 5 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9FAK CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38 in a desensitised state (StateD2) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 668–700（33 aa）	Not recorded	HEX HEXANE × 6 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 5 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 5 D10 DECANE × 7 PLM PALMITIC ACID × 8 CL CHLORIDE ION × 4 ABU GAMMA-AMINO-BUTANOIC ACID × 2 R16 HEXADECANE × 3 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9FAM CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38 in a desensitised state (StateD3) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain H 668–700（33 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 2 CL CHLORIDE ION × 3 HEX HEXANE × 7 D10 DECANE × 1 PLM PALMITIC ACID × 1 CLR CHOLESTEROL × 1 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9FAN CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 668–700（33 aa）	Not recorded	PLM PALMITIC ACID × 1 CLR CHOLESTEROL × 1 D10 DECANE × 1 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9FAP CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC1) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain H 668–700（33 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 5 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 2 PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 1 D10 DECANE × 1 HEX HEXANE × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9FAQ CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC2) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain H 668–700（33 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 5 D10 DECANE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PLM PALMITIC ACID × 5 CLR CHOLESTEROL × 1 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 1 HEX HEXANE × 2 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9FAR CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from a closed state, obtained by focused refinement Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 668–700（33 aa）	Not recorded	PLM PALMITIC ACID × 1 CLR CHOLESTEROL × 1 D10 DECANE × 1 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 CL CHLORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9FAT CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain H 668–700（33 aa）	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 3 D10 DECANE × 3 CL CHLORIDE ION × 2 R16 HEXADECANE × 1 HEX HEXANE × 3 PLM PALMITIC ACID × 1 CLR CHOLESTEROL × 1 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 1 A8W Pregnenolone sulfate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9FAU CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC1) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain H 668–700（33 aa）	Not recorded	HEX HEXANE × 6 D10 DECANE × 6 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 2 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 R16 HEXADECANE × 3 PLM PALMITIC ACID × 2 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9FAV CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2 and Megabody25, in a closed state (StateC2) Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain H 668–700（33 aa）	Not recorded	HEX HEXANE × 5 D10 DECANE × 4 R16 HEXADECANE × 3 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9FAW CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, HEPES and Megabody25, in a desensitised state Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain H 668–700（33 aa）	Not recorded	HEX HEXANE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9FAX CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state Deposited 2024-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain G 668–700（33 aa） Chain H 668–700（33 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 R16 HEXADECANE × 5 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 2 CLR CHOLESTEROL × 2 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 HEX HEXANE × 13 D10 DECANE × 5 PLM PALMITIC ACID × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；15 mM Hepes pH 7.4, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NLGN2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–573； UniProt 42–611

MAM domain-containing glycosylphosphatidylinositol anchor protein 1

Homo sapiens

UniProt Q8NFP4

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 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 19–330	Fragment：UNP residues 19-330	Neuroligin-2 × 2 （Q8NFZ4） 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	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；300mM Ammonium citrate tribasic, pH 7.0, 13% 1,3-Butanediol and 18%(v/v) PEG3350	Resolution 3.14 Å R-free 0.278

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 5XEQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5V5V Complex of NLGN2 with MDGA1 Ig1-Ig2 Deposited 2017-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 22–237（216 aa） Chain H 22–237（216 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.05 M HEPES pH 7.5, 0.05 M MOPS pH 7.5, 12 % (v/v) ethylene glycol, 9 % (w/v) PEG 8000	Resolution 4.11 Å R-free 0.319
5V5V Complex of NLGN2 with MDGA1 Ig1-Ig2 Deposited 2017-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 22–237（216 aa） Chain L 22–237（216 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.05 M HEPES pH 7.5, 0.05 M MOPS pH 7.5, 12 % (v/v) ethylene glycol, 9 % (w/v) PEG 8000	Resolution 4.11 Å R-free 0.319
5V5V Complex of NLGN2 with MDGA1 Ig1-Ig2 Deposited 2017-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 22–237（216 aa） Chain J 22–237（216 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.05 M HEPES pH 7.5, 0.05 M MOPS pH 7.5, 12 % (v/v) ethylene glycol, 9 % (w/v) PEG 8000	Resolution 4.11 Å R-free 0.319
5V5W Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges Deposited 2017-03-15	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 22–237（216 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M ammonium sulfate, 3.72% (v/v) 2-propanol, 25% (v/v) glycerol	Resolution 2.72 Å R-free 0.256
5V5W Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges Deposited 2017-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 22–237（216 aa）	Not recorded	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M ammonium sulfate, 3.72% (v/v) 2-propanol, 25% (v/v) glycerol	Resolution 2.72 Å R-free 0.256

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

View Construct and Data Evidence

UniProt name	MDGA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–315； UniProt 19–330

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5xeq
Deposition date deposition_date	2017-04-05
Structure title title	Crystal Structure of human MDGA1 and human neuroligin-2 complex
Keywords keywords	Immunogloubulin-like domain, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.77 Å
Radius of gyration Rg (electron density) rg_electron	34.46 Å
Forward intensity I(0) i0	132390000.00
Molecular weight molecular_weight	91474.0 kDa
Excluded volume excluded_volume	114410 Å³
Envelope volume envelope_volume	154680 Å³
Hydration-shell volume shell_volume	39729 Å³
Envelope diameter envelope_diameter	136.0 Å
Shell Rg shell_rg	38.26 Å
Envelope Rg envelope_rg	35.02 Å
Shape Rg shape_rg	34.39 Å
Total Rg total_rg	34.97 Å
Total atoms total_atoms	6450
Residues n_residues	817
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	127.9 Å
Rg (real space) rg_real	35.04 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	1.3240e+08
I(0) uncertainty (real space) i0_real_error	2.3150e+06
Rg (reciprocal space) rg_reciprocal	34.87 Å
I(0) (reciprocal space) i0_reciprocal	132400000.0000
Solution quality estimate total_estimate	0.8277
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.1 Å
Skewness Skewness skewness	0.594
Kurtosis Kurtosis kurtosis	-0.011
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16920000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.651; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.963

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neuroligin-2
Molecular weight formula_weight	64101.1 kDa
Mutation mutation	N98Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6450

ADPPVVNTAYGRVRGVRRELNNEILGPVVQFLGVPYATPPLGARRFQPPEAPASWPGVRQATTLPPACPQNLHGALPAIMLPVWFTDNLEAAATYVQNQSEDCLYLNLYVPTEDGPLTKKRDEATLNPPDTDIRDPGKKPVMLFLHGGSYMEGTGNMFDGSVLAAYGNVIVATLNYRLGVLGFLSTGDQAAKGNYGLLDQIQALRWLSENIAHFGGDPERITIFGSGAGASCVNLLILSHHSEGLFQKAIAQSGTAISSWSVNYQPLKYTRLLAAKVGCDREDSAEAVECLRRKPSRELVDQDVQPARYHIAFGPVVDGDVVPDDPEILMQQGEFLNYDMLIGVNQGEGLKFVEDSAESEDGVSASAFDFTVSNFVDNLYGYPEGKDVLRETIKFMYTDWADRDNGEMRRKTLLALFTDHQWVAPAVATAKLHADYQSPVYFYTFYHHCQAEGRPEWADAAHGDELPYVFGVPMVGATDLFPCNFSKNDVMLSAVVMTYWTNFAKTGDPNQPVPQDTKFIHTKPNRFEEVVWSKFNSKEKQYLHIGLKPRVRDNYRANKVAFWLELVPHLHNLVPR

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	MAM domain-containing glycosylphosphatidylinositol anchor protein 1
Molecular weight formula_weight	35038.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADPQGVYAPAQAQIVHAGQACVVKEDNISERVYTIREGDTLMLQCLVTGHPRPQVRWTKTAGSASDKFQETSVFNETLRIERIARTQGGRYYCKAENGVGVPAIKSIRVDVQYLDEPMLTVHQTVSDVRGNFYQEKTVFLRCTVNSNPPARFIWKRGSDTLSHSQDNGVDIYEPLYTQGETKVLKLKNLRPQDYASYTCQVSVRNVCGIPDKAITFRLTNTTAPPALKLSVNETLVVNPGENVTVQCLLTGGDPLPQLQWSHGPGPLPLGALAQGGTLSIPSVQARDSGYYNCTATNNVGNPAKKTVNLLVRSMKLVPR

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	Spodoptera frugiperda

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	1

Entity 4 Entity 4 non-polymer

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

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5xeqA00
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	5xeqB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5xeqB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5xeqB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	154.875 Å
Unit-cell length b length_b	69.134 Å
Unit-cell length c length_c	108.843 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.136 Å
Low-resolution limit resolution_low	49.199 Å
R factor r_factor	0.2385
R_work r_work	0.2341
R_free r_free	0.2779

fit	/app/data/saxs_computation/xe/5xeq/5xeq.fit
pddf	/app/data/pr_computation/xe/5xeq/5xeq.pr.out
profile	/app/data/saxs_computation/xe/5xeq/5xeq.dat

Crystal Structure of human MDGA1 and human neuroligin-2 complex

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

Neuroligin-2

State in the Current Structure

Other States of the Same Protein in the Database

MAM domain-containing glycosylphosphatidylinositol anchor protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 branched

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)