SAXSdb — 2d3k

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

Peptidyl-tRNA hydrolase

Pyrococcus horikoshii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTH_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121 Author chain B； PDBConstruct 1–121； UniProt 1–121

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	2d3k
Deposition date deposition_date	2005-09-29
Structure title title	Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3
Keywords keywords	;HYDROLASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; HYDROLASE
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.

2d3k__assembly_1__model_1

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

Download this curve (.dat)

2d3k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d3k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.06 Å
Rg (electron density)	16.90 Å
Total Rg	18.17 Å
Atom count	1840
Residues	236
Excluded volume	33617 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d3k__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Peptidyl-tRNA hydrolase
Molecular weight formula_weight	13398.8 kDa
EC 编号 ec_number	3.1.1.29
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	2122

MIKMFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAWFREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTVLAVGPAPEEIVDKVTGNLKLL

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2d3ka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

Domain ID domain_id	d2d3kb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.131 — Peptidyl-tRNA hydrolase II
Superfamily Superfamily superfamily	c.131.1 — Peptidyl-tRNA hydrolase II
Family Family family	c.131.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2d3kA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

Domain ID domain_id	2d3kB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1490 — Bit1
Homologous superfamily homologous superfamily	10 — Bit1

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Unit-cell length a length_a	59.855 Å
Unit-cell length b length_b	59.855 Å
Unit-cell length c length_c	128.237 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	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	32.060 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2550

Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3

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

Peptidyl-tRNA hydrolase

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

2d3k__assembly_1__model_1

2d3k__assembly_1__model_1 | I(q)

2d3k__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3

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

Peptidyl-tRNA hydrolase

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

2d3k__assembly_1__model_1

2d3k__assembly_1__model_1 | I(q)

2d3k__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)