2dyy

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

Method: X-RAY DIFFRACTION

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

UPF0076 protein PH0854

Pyrococcus horikoshii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y854_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 1–126 Author chain B； PDBConstruct 1–126； UniProt 1–126 Author chain C； PDBConstruct 1–126； UniProt 1–126 Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain E； PDBConstruct 1–126； UniProt 1–126 Author chain F； PDBConstruct 1–126； UniProt 1–126 Author chain G； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126 Author chain I； PDBConstruct 1–126； UniProt 1–126 Author chain J； PDBConstruct 1–126； UniProt 1–126 Author chain K； PDBConstruct 1–126； UniProt 1–126 Author chain L； PDBConstruct 1–126； UniProt 1–126

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	2dyy
Deposition date deposition_date	2006-09-19
Structure title title	Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii
Keywords keywords	;Putative translation initiation inhibitor, Pyrococcus horikoshii, trimer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2dyy__assembly_1__model_1

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

Download this curve (.dat)

2dyy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dyy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.86 Å
Rg (electron density)	19.29 Å
Total Rg	20.39 Å
Atom count	2814
Residues	363
Excluded volume	50994 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dyy__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dyy__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dyy__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dyy__assembly_4__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2dyya_
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	d2dyyb_
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	d2dyyc_
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	d2dyyd_
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	d2dyye_
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	d2dyyf_
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	d2dyyg_
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	d2dyyh_
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	d2dyyi_
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	d2dyyj_
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	d2dyyk_
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	d2dyyl_
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 (12 domains)

Domain ID domain_id	2dyyA00
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	2dyyB00
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	2dyyC00
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	2dyyD00
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	2dyyE00
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	2dyyF00
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	2dyyG00
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	2dyyH00
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	2dyyI00
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	2dyyJ00
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	2dyyK00
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	2dyyL00
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	92.490 Å
Unit-cell length b length_b	43.090 Å
Unit-cell length c length_c	170.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.730 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2950

Description description	UPF0076 protein PH0854
Molecular weight formula_weight	14052.2 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	11461

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

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

UPF0076 protein PH0854

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

2dyy__assembly_1__model_1

2dyy__assembly_1__model_1 | I(q)

2dyy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	233

Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii

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

UPF0076 protein PH0854

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

2dyy__assembly_1__model_1

2dyy__assembly_1__model_1 | I(q)

2dyy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)