SAXSdb — 2f62

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

Nucleoside 2-deoxyribosyltransferase

Trypanosoma brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 (2-ETHYLPHENYL)METHANOL × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q57VC7_9TRYP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–161； UniProt 1–153 Author chain B； PDBConstruct 9–161； UniProt 1–153

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	2f62
Deposition date deposition_date	2005-11-28
Structure title title	Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound
Keywords keywords	;SGPP, Structural GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE NDRT, Nucleoside 2-deoxyribosyltransferase, Trypanosoma brucei, Structural Genomics of Pathogenic Protozoa Consortium, TRANSFERASE ;; TRANSFERASE
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.

2f62__assembly_1__model_1

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

Download this curve (.dat)

2f62__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f62__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.44 Å
Rg (electron density)	20.16 Å
Total Rg	20.89 Å
Atom count	2565
Residues	302
Excluded volume	45617 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f62__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 (5)

Entity 1 Entity 1 polymer

Description description	Nucleoside 2-deoxyribosyltransferase
Molecular weight formula_weight	18664.1 kDa
EC 编号 ec_number	2.4.2.6
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	2983

MAHHHHHHMRKIYIAGPAVFNPDMGASYYNKVRELLKKENVMPLIPTDNEATEALDIRQKNIQMIKDCDAVIADLSPFRGHEPDCGTAFEVGCAAALNKMVLTFTSDRRNMREKYGSGVDKDNLRVEGFGLPFNLMLYDGVEVFDSFESAFKYFLANFPSK

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	(2-ETHYLPHENYL)METHANOL
Molecular weight formula_weight	136.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2f62a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
Family Family family	c.23.14.1 — N-deoxyribosyltransferase

Domain ID domain_id	d2f62a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2f62b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
Family Family family	c.23.14.1 — N-deoxyribosyltransferase

Domain ID domain_id	d2f62b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2f62A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	2f62B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

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Unit-cell length a length_a	58.614 Å
Unit-cell length b length_b	75.913 Å
Unit-cell length c length_c	85.957 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1675
R_work r_work	0.1665
R_free r_free	0.1863

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound

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

Nucleoside 2-deoxyribosyltransferase

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

2f62__assembly_1__model_1

2f62__assembly_1__model_1 | I(q)

2f62__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.5 A resolution with (2-ETHYLPHENYL)METHANOL bound

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

Nucleoside 2-deoxyribosyltransferase

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

2f62__assembly_1__model_1

2f62__assembly_1__model_1 | I(q)

2f62__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)