SAXSdb — 2dpl

▼

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

GMP synthase [glutamine-hydrolyzing] subunit B

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	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GUAAB_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–308； UniProt 1–308 Author chain B； PDBConstruct 1–308； UniProt 1–308

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2dpl
Deposition date deposition_date	2006-05-12
Structure title title	Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3
Keywords keywords	;Pyrococcus horikoshii OT3, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LIGASE ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2dpl__assembly_1__model_1

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

Download this curve (.dat)

2dpl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dpl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.21 Å
Rg (electron density)	31.14 Å
Total Rg	31.43 Å
Atom count	4477
Residues	565
Excluded volume	80629 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dpl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2dpla1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.0 — automated matches

Domain ID domain_id	d2dpla2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.2 — GMP synthetase C-terminal dimerisation domain
Family Family family	d.52.2.0 — automated matches

Domain ID domain_id	d2dplb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.0 — automated matches

Domain ID domain_id	d2dplb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.2 — GMP synthetase C-terminal dimerisation domain
Family Family family	d.52.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2dplA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2dplA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2dplB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2dplB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	70.400 Å
Unit-cell length b length_b	83.334 Å
Unit-cell length c length_c	112.255 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.430 Å
Low-resolution limit resolution_low	29.820 Å
R factor r_factor	0.2370
R_work r_work	0.2360
R_free r_free	0.2490

Description description	GMP synthase [glutamine-hydrolyzing] subunit B
Molecular weight formula_weight	34609.9 kDa
EC 编号 ec_number	6.3.5.2
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5452

Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3

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

GMP synthase [glutamine-hydrolyzing] subunit B

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

2dpl__assembly_1__model_1

2dpl__assembly_1__model_1 | I(q)

2dpl__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
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	952

Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3

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

GMP synthase [glutamine-hydrolyzing] subunit B

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

2dpl__assembly_1__model_1

2dpl__assembly_1__model_1 | I(q)

2dpl__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)