SAXSdb — 9q0o

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

Amidophosphoribosyltransferase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	ADP-sugar pyrophosphatase × 4 （Q9UKK9） IRON/SULFUR CLUSTER × 4 6-(benzylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–506； UniProt 12–517 Author chain B； PDBConstruct 1–506； UniProt 12–517 Author chain C； PDBConstruct 1–506； UniProt 12–517 Author chain D； PDBConstruct 1–506； UniProt 12–517

ADP-sugar pyrophosphatase

Homo sapiens

UniProt Q9UKK9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Amidophosphoribosyltransferase × 4 （Q06203） IRON/SULFUR CLUSTER × 4 6-(benzylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUDT5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 6–223； UniProt 2–219 Author chain F； PDBConstruct 6–223； UniProt 2–219 Author chain G； PDBConstruct 6–223； UniProt 2–219 Author chain H； PDBConstruct 6–223； UniProt 2–219

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	9q0o
Deposition date deposition_date	2025-08-13
Structure title title	Cryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinosine-5'-monophosphate (6-benzylTIMP)
Keywords keywords	Purine synthesis, phosphoribosyltransferase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

9q0o__assembly_1__model_1

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

Download this curve (.dat)

9q0o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9q0o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.43 Å
Rg (electron density)	44.68 Å
Total Rg	44.99 Å
Atom count	21796
Residues	2780
Excluded volume	389550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9q0o__assembly_1__model_1`	octameric （8）	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 (4)

Entity 1 Entity 1 polymer

Description description	Amidophosphoribosyltransferase
Molecular weight formula_weight	60690.3 kDa
EC 编号 ec_number	2.4.2.14
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21796

CGVFGCIASGEWPTQLDVPHVITLGLVGLQHRGQESAGIVTSDGSSVPTFKSHKGMGLVNHVFTEDNLKKLYVSNLGIGHTRYATTGKCELENCQPFVVETLHGKIAVAHNGELVNAARLRKKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKEAPTAYSLLIMHRDVIYAVRDPYGNRPLCIGRLIPVSDINDKEKKTSETEGWVVSSESCSFLSIGARYYREVLPGEIVEISRHNVQTLDIISRSEGNPVAFCIFEYVYFARPDSMFEDQMVYTVRYRCGQQLAIEAPVDADLVSTVPESATPAALAYAGKCGLPYVEVLCKNRYVGRTFIQPNMRLRQLGVAKKFGVLSDNFKGKRIVLVDDSIVRGNTISPIIKLLKESGAKEVHIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVYLSVEGLVSSVQEGIKFKKQKEKKHDIMIQENGNGLECFEKSGHCTACLTGKYPVELEWGGSKPIPNPLLGLDSTSAWSHPQFEKGGGSGGGSGGGAWSHPQFEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	ADP-sugar pyrophosphatase
Molecular weight formula_weight	24523.7 kDa
EC 编号 ec_number	3.6.1.13,3.6.1.58,2.7.7.96
Mutation mutation	Y74F
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GGGSGESQEPTESSQNGKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVAVIPVLQRTLHFECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANAKPFEVPFLKF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	6-(benzylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
Molecular weight formula_weight	454.4 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	502672

Cryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinosine-5'-monophosphate (6-benzylTIMP)

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

Amidophosphoribosyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

ADP-sugar pyrophosphatase

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

9q0o__assembly_1__model_1

9q0o__assembly_1__model_1 | I(q)

9q0o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Cryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinosine-5'-monophosphate (6-benzylTIMP)

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

Amidophosphoribosyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ADP-sugar pyrophosphatase

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

9q0o__assembly_1__model_1

9q0o__assembly_1__model_1 | I(q)

9q0o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)