SAXSdb — 4tk3

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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 4	Gamma-aminobutyric acid receptor subunit alpha-3 × 2 （P20236） water × 2	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 344–762 Author chain B； PDBConstruct 1–419； UniProt 344–762

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 4	Gephyrin × 2 （Q03555） water × 2	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 C； PDBConstruct 1–11； UniProt 396–406 Author chain D； PDBConstruct 1–11； UniProt 396–406

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	4tk3
Deposition date deposition_date	2014-05-25
Structure title title	Geph E in complex with a GABA receptor alpha3 derived double mutant peptide in spacegroup P21212
Keywords keywords	;Scaffolding protein, Neurotransmitter receptor anchoring, Molybdenum co factor bio synthesis, structural protein, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC 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.

4tk3__assembly_1__model_1

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

Download this curve (.dat)

4tk3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4tk3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.17 Å
Rg (electron density)	31.70 Å
Total Rg	32.09 Å
Atom count	6421
Residues	841
Excluded volume	115040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4tk3__assembly_1__model_1`	tetrameric （4）	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 (3)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6465

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	1223.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

FSIVGTLYPIN

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4tk3A01
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	4tk3A02
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	4tk3A03
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	4tk3A04
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

Domain ID domain_id	4tk3B01
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	4tk3B02
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	4tk3B03
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	4tk3B04
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	110.027 Å
Unit-cell length b length_b	157.184 Å
Unit-cell length c length_c	51.026 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	48.533 Å
R factor r_factor	0.2307
R_work r_work	0.2287
R_free r_free	0.2666

Geph E in complex with a GABA receptor alpha3 derived double mutant peptide in spacegroup P21212

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

4tk3__assembly_1__model_1

4tk3__assembly_1__model_1 | I(q)

4tk3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Geph E in complex with a GABA receptor alpha3 derived double mutant peptide in spacegroup P21212

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

4tk3__assembly_1__model_1

4tk3__assembly_1__model_1 | I(q)

4tk3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)