SAXSdb — 4u91

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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 monomer	Monomer	Protein 1	ACETATE ION × 1 1,2-ETHANEDIOL × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GEPH_RAT
Isoform	Q03555-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 344–762

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	4u91
Deposition date deposition_date	2014-08-05
Structure title title	GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric peptide
Keywords keywords	Transferase, Scaffolding protein, Inhibitory synapse, GABA type A receptor, transfer protein - structural protein complex; TRANSFER 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.

4u91__assembly_1__model_1

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

Download this curve (.dat)

4u91__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u91__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.88 Å
Rg (electron density)	31.60 Å
Total Rg	31.84 Å
Atom count	3173
Residues	415
Excluded volume	56780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u91__assembly_1__model_1`	Monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4u91__assembly_2__model_1`	Dimeric （2）	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 (7)

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	3689

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	Glycine receptor subunit beta
Molecular weight formula_weight	1194.4 kDa
Mutation mutation	Additional Cysteine at the C terminus
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

FSIVGSLPRDC

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 6 Entity 6 non-polymer

Description description	1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione)
Molecular weight formula_weight	268.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4u91A01
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	4u91A02
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	4u91A03
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	4u91A04
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	87.440 Å
Unit-cell length b length_b	99.210 Å
Unit-cell length c length_c	112.490 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	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1714
R_work r_work	0.1685
R_free r_free	0.2256

GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4u91__assembly_1__model_1

4u91__assembly_1__model_1 | I(q)

4u91__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4u91__assembly_1__model_1

4u91__assembly_1__model_1 | I(q)

4u91__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)