SAXSdb — 3r6c

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

Anthranilate phosphoribosyltransferase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 1 MAGNESIUM ION × 2 8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 1 MAGNESIUM ION × 2 8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRPD_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–369； UniProt 2–370 Author chain B； PDBConstruct 1–369； UniProt 2–370

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	3r6c
Deposition date deposition_date	2011-03-21
Structure title title	Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS179)
Keywords keywords	;Anthranilate Phosphoribosyltransferase, Anthranilic Acids, Magnesium, Tryptophan, Structural Genomics, TB Structural Genomics Consortium, TBSGC, Transferase-transferase inhibitor complex ;; Transferase/transferase inhibitor
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.

3r6c__assembly_1__model_1

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

Download this curve (.dat)

3r6c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r6c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.38 Å
Rg (electron density)	19.32 Å
Total Rg	20.15 Å
Atom count	2579
Residues	346
Excluded volume	45452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r6c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3r6c__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Anthranilate phosphoribosyltransferase
Molecular weight formula_weight	38717.7 kDa
EC 编号 ec_number	2.4.2.18
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	5711

ALSAEGSSGGSRGGSPKAEAASVPSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQILEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
Molecular weight formula_weight	390.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid
Molecular weight formula_weight	340.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	572

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3r6cA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

Domain ID domain_id	3r6cA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	3r6cB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

Domain ID domain_id	3r6cB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

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Unit-cell length a length_a	93.982 Å
Unit-cell length b length_b	77.930 Å
Unit-cell length c length_c	99.803 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.18 °
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	1.830 Å
Low-resolution limit resolution_low	93.680 Å
R factor r_factor	0.1881
R_work r_work	0.1861
R_free r_free	0.2265

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS179)

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

Anthranilate phosphoribosyltransferase

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

3r6c__assembly_1__model_1

3r6c__assembly_1__model_1 | I(q)

3r6c__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS179)

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

Anthranilate phosphoribosyltransferase

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

3r6c__assembly_1__model_1

3r6c__assembly_1__model_1 | I(q)

3r6c__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)