SAXSdb — 2hry

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

Phosphoribosylformylglycinamidine synthase II

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 2 PHOSPHATE ION × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PURL_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–603； UniProt 1–603

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	2hry
Deposition date deposition_date	2006-07-20
Structure title title	T. maritima PurL complexed with AMPPCP
Keywords keywords	beta barrel; alpha-beta structure, ligase; LIGASE
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.

2hry__assembly_1__model_1

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

Download this curve (.dat)

2hry__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hry__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.89 Å
Rg (electron density)	24.25 Å
Total Rg	25.03 Å
Atom count	4467
Residues	575
Excluded volume	79822 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hry__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Phosphoribosylformylglycinamidine synthase II
Molecular weight formula_weight	65976.5 kDa
EC 编号 ec_number	6.3.5.3
Mutation mutation	His72Ala
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	4703

MKLRYLNILKEKLGREPTFVELQAFSVMWSEHCGYSHTKKYIRRLPKTGFEGNAGVVNLDDYYSVAFKIESANHPSAIEPYNGAATGVGGIIRDVLAMGARPTAIFDSLHMSRIIDGIIEGIADYGNSIGVPTVGGELRISSLYAHNPLVNVLAAGVVRNDMLVDSKASRPGQVIVIFGGATGRDGIHGASFASEDLTGDKATKLSIQVGDPFAEKMLIEAFLEMVEEGLVEGAQDLGAGGVLSATSELVAKGNLGAIVHLDRVPLREPDMEPWEILISESQERMAVVTSPQKASRILEIARKHLLFGDVVAEVIEEPVYRVMYRNDLVMEVPVQLLANAPEEDIVEYTPGKIPEFKRVEFEEVNAREVFEQYDHMVGTDTVVPPGFGAAVMRIKRDGGYSLVTHSRADLALQDTYWGTLIAVLESVRKTLSVGAEPLAITNCVNYGDPDVDPVGLSAMMTALKNACEFSGVPVASGNASLYNTYQGKPIPPTLVVGMLGKVNPQKVAKPKPSKVFAVGWNDFELEREKELWRAIRKLSEEGAFILSSSQLLTRTHVETFREYGLKIEVKLPEVRPAHQMVLVFSERTPVVDVPVKEIGTLSR

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	236

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hrya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d2hrya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d2hrya3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d2hrya4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	2hryA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	2hryA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	2hryA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	2hryA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1670 — Formylglycinamide ribonucleotide amidotransferase, C-terminal domain

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Unit-cell length a length_a	56.617 Å
Unit-cell length b length_b	69.997 Å
Unit-cell length c length_c	133.476 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2830

T. maritima PurL complexed with AMPPCP

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

Phosphoribosylformylglycinamidine synthase II

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

2hry__assembly_1__model_1

2hry__assembly_1__model_1 | I(q)

2hry__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

T. maritima PurL complexed with AMPPCP

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

Phosphoribosylformylglycinamidine synthase II

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

2hry__assembly_1__model_1

2hry__assembly_1__model_1 | I(q)

2hry__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)