1oni

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

Method: X-RAY DIFFRACTION

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

14.5 kDa translational inhibitor protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	BENZOIC ACID × 5 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	BENZOIC ACID × 4 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	BENZOIC ACID × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UK14_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–138； UniProt 2–137 Author chain B； PDBConstruct 3–138； UniProt 2–137 Author chain C； PDBConstruct 3–138； UniProt 2–137 Author chain D； PDBConstruct 3–138； UniProt 2–137 Author chain E； PDBConstruct 3–138； UniProt 2–137 Author chain F； PDBConstruct 3–138； UniProt 2–137 Author chain G； PDBConstruct 3–138； UniProt 2–137 Author chain H； PDBConstruct 3–138； UniProt 2–137 Author chain I； PDBConstruct 3–138； UniProt 2–137

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	1oni
Deposition date deposition_date	2003-02-28
Structure title title	Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family
Keywords keywords	YjgF/YER057c/UK114 family, Trichloroacetic acid soluble protein, Translational inhibitor, TRANSLATION; TRANSLATION
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.

1oni__assembly_1__model_1

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

Download this curve (.dat)

1oni__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1oni__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.00 Å
Rg (electron density)	19.53 Å
Total Rg	20.60 Å
Atom count	3044
Residues	404
Excluded volume	54717 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1oni__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1oni__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1oni__assembly_3__model_1`	trimeric （3）	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	14.5 kDa translational inhibitor protein
Molecular weight formula_weight	14519.5 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	9553

GSSSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGVAEEAKQALKNMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAALPKGSRIEIEAVAIQGPLTTASL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BENZOIC ACID
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	443

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1onia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onid_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onie_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onif_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onig_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onih_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

Domain ID domain_id	d1onii_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.1 — YjgF-like
Family Family family	d.79.1.1 — YjgF/L-PSP

CATH v4.4 (9 domains)

Domain ID domain_id	1oniA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

Domain ID domain_id	1oniI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	40 — RutC-like

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Unit-cell length a length_a	154.158 Å
Unit-cell length b length_b	154.158 Å
Unit-cell length c length_c	104.559 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	54

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1850
R_free r_free	0.2160

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

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

14.5 kDa translational inhibitor protein

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

1oni__assembly_1__model_1

1oni__assembly_1__model_1 | I(q)

1oni__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

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

14.5 kDa translational inhibitor protein

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

1oni__assembly_1__model_1

1oni__assembly_1__model_1 | I(q)

1oni__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)