6hsn

Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide

Method: X-RAY DIFFRACTION

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

Gephyrin

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Gamma-aminobutyric acid receptor subunit alpha-3 × 4 （P20236） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 ACETATE ION × 16 PHOSPHATE ION × 2 SODIUM ION × 2 1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione) × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GEPH_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 350–768

Gamma-aminobutyric acid receptor subunit alpha-3

OrganismNot specified

UniProt P20236

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Gephyrin × 2 （Q03555） ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 ACETATE ION × 16 PHOSPHATE ION × 2 SODIUM ION × 2 1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione) × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GBRA3_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–10； UniProt 396–405 Author chain E； PDBConstruct 1–10； UniProt 396–405

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	6hsn
Deposition date deposition_date	2018-10-01
Structure title title	Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide
Keywords keywords	Gephyrin, GABAA receptor, moonlighting protein, Scaffolding protein, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6hsn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6hsn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hsn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.74 Å
Rg (electron density)	32.21 Å
Total Rg	32.54 Å
Atom count	13670
Residues	862
Excluded volume	121820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hsn__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Gephyrin
Molecular weight formula_weight	45652.4 kDa
EC 编号 ec_number	2.7.7.75,2.10.1.1
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	7895

MSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Gamma-aminobutyric acid receptor subunit alpha-3
Molecular weight formula_weight	1114.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

FNIVGTTYPC

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione)
Molecular weight formula_weight	308.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	480

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6hsnA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
Homologous superfamily homologous superfamily	10 — MoaB/Mog-like domain

Domain ID domain_id	6hsnA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
Homologous superfamily homologous superfamily	10 — Molybdopterin biosynthesis moea protein, domain 2

Domain ID domain_id	6hsnA03
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	190 — Molybdopterin biosynthesis moeA protein; domain 3
Homologous superfamily homologous superfamily	11 — Molybdopterin biosynthesis moea protein, domain 3.

Domain ID domain_id	6hsnA04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	340 — Beta-clip
Homologous superfamily homologous superfamily	10 — MoeA, C-terminal, domain IV

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Unit-cell length a length_a	86.962 Å
Unit-cell length b length_b	99.217 Å
Unit-cell length c length_c	111.608 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1608
R_work r_work	0.1590
R_free r_free	0.1958

Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide

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

Gephyrin

State in the Current Structure

Other States of the Same Protein in the Database

Gamma-aminobutyric acid receptor subunit alpha-3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6hsn__assembly_1__model_1

6hsn__assembly_1__model_1 | I(q)

6hsn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide

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

Gephyrin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Gamma-aminobutyric acid receptor subunit alpha-3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6hsn__assembly_1__model_1

6hsn__assembly_1__model_1 | I(q)

6hsn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)