SAXSdb — 9xuu

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

Poxin-Schlafen

Monkeypox virus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–195 Chain B； UniProt 1–195	Not recorded	C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BICINE pH 8.5, 8% w/v Polyethylene glycol monomethyl ether 5,000	Resolution 1.94 Å R-free 0.202
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–195 Chain D； UniProt 1–195	Not recorded	C2E 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BICINE pH 8.5, 8% w/v Polyethylene glycol monomethyl ether 5,000	Resolution 1.94 Å R-free 0.202

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9XUU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8C9K Structure of Mpox virus poxin Deposited 2023-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM HEPES pH 7.5, 10% (w/v) PEG 8000	Resolution 1.72 Å R-free 0.228
8C9K Structure of Mpox virus poxin Deposited 2023-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM HEPES pH 7.5, 10% (w/v) PEG 8000	Resolution 1.72 Å R-free 0.228
8ORV Crystal structure of monkeypox virus poxin in complex with the STING agonist MD1203 Deposited 2023-04-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa）	Not recorded	VZ6 9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；40% (v/v) PEG 300; 0.1M phosphate-citrate, pH 4.2	Resolution 1.65 Å R-free 0.224
8P44 Crystal structure of monkeypox virus poxin in complex with the STING agonist MD1202D Deposited 2023-05-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	WY8 9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM ammonium nitrate, 20% w/v PEG 3.350	Resolution 1.93 Å R-free 0.261
8P44 Crystal structure of monkeypox virus poxin in complex with the STING agonist MD1202D Deposited 2023-05-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	WY8 9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM ammonium nitrate, 20% w/v PEG 3.350	Resolution 1.93 Å R-free 0.261
9XUJ Crystal structure of MPXV poxin Deposited 2025-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350	Resolution 1.75 Å R-free 0.235
9XUJ Crystal structure of MPXV poxin Deposited 2025-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350	Resolution 1.75 Å R-free 0.235
9XUP Crystal structure of MPXV poxin in complex with Gp[2'-5']Ap[3'] Deposited 2025-11-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	9BG 2',5'-GpAp × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25% w/v Polyethylene glycol 1,500	Resolution 2.01 Å R-free 0.227
9XUT Crystal structure of MPXV poxin in complex with 3'3'-cGAMP Deposited 2025-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–195（195 aa） Chain B 1–195（195 aa）	Not recorded	4BW 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.5, 12% w/v Polyethylene glycol 3,350	Resolution 1.81 Å R-free 0.216
9XUT Crystal structure of MPXV poxin in complex with 3'3'-cGAMP Deposited 2025-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	4BW 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES pH 7.5, 12% w/v Polyethylene glycol 3,350	Resolution 1.81 Å R-free 0.216

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POXIN_MONPV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–198； UniProt 1–195 Author chain B； PDBConstruct 4–198； UniProt 1–195 Author chain C； PDBConstruct 4–198； UniProt 1–195 Author chain D； PDBConstruct 4–198； UniProt 1–195

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	9xuu
Deposition date deposition_date	2025-11-25
最后修订 last_revision	2026-05-27
Structure title title	Crystal structure of MPXV poxin in complex with c-di-GMP
Keywords keywords	Enzyme, c-di-GMP, degradation, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.86 Å
Radius of gyration Rg (electron density) rg_electron	34.63 Å
Forward intensity I(0) i0	123504000.00
Molecular weight molecular_weight	89322.0 kDa
Excluded volume excluded_volume	111750 Å³
Envelope volume envelope_volume	146230 Å³
Hydration-shell volume shell_volume	35952 Å³
Envelope diameter envelope_diameter	115.6 Å
Shell Rg shell_rg	40.33 Å
Envelope Rg envelope_rg	34.22 Å
Shape Rg shape_rg	34.63 Å
Total Rg total_rg	35.05 Å
Total atoms total_atoms	6288
Residues n_residues	780
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.2 Å
Rg (real space) rg_real	35.01 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.2350e+08
I(0) uncertainty (real space) i0_real_error	2.1880e+06
Rg (reciprocal space) rg_reciprocal	34.93 Å
I(0) (reciprocal space) i0_reciprocal	123500000.0000
Solution quality estimate total_estimate	0.8683
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.675
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22390000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.856; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Poxin-Schlafen
Molecular weight formula_weight	22421.7 kDa
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	7164

SGGMFYAHAFGGYDENLHAFPGISSTVANDVRKYSVVSVYNKKYNIVKNKYMWCNSQVNKRYIGALLPMFECNEYLQIGDPIHDLEGNQISIVTYRHKNYYALSGIGYESLDLCLEGVGIHHHVLETGNAVYGKVQHEYSTIKEKAKEMNALKPGPIIDYHVWIGDCVCQVTTVDVHGKEIMRMRFKRGAVLPIPNLV

来源 Source

来源生物 organism	Monkeypox virus
NCBI Class编号 ncbi_taxonomy_id	10244
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ;
Molecular weight formula_weight	690.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	832

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8. Citations (1)

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Unit-cell length a length_a	54.290 Å
Unit-cell length b length_b	91.700 Å
Unit-cell length c length_c	93.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	46.810 Å
R factor r_factor	0.1633
R_work r_work	0.1613
R_free r_free	0.2022

fit	/app/data/saxs_computation/xu/9xuu/9xuu.fit
pddf	/app/data/pr_computation/xu/9xuu/9xuu.pr.out
profile	/app/data/saxs_computation/xu/9xuu/9xuu.dat

Crystal structure of MPXV poxin in complex with c-di-GMP

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

Poxin-Schlafen

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction