1azy

STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE

Method: X-RAY DIFFRACTION D_max: 122.4 Å Quality: GOOD

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

THYMIDINE PHOSPHORYLASE

OrganismNot specified

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 2–440 Chain B； UniProt 2–440	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；pH 4.6	Resolution 3.00 Å R-free 0.276

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 1AZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OTP STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–440（439 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；PROTEIN WAS CRYSTALLIZED FROM 0.9 - 1.2 M SODIUM CITRATE (PH 6.4 - 6.8) AND 2MM DTT AT ROOM TEMPERATURE USING HANGING DROP METHOD	Resolution 2.80 Å R-free 0.248
1TPT THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION Deposited 1990-06-14	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 1–441（441 aa）	Not recorded	SO4 SULFATE ION × 2 TDR THYMINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
2TPT STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE Deposited 1997-11-24	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 2–440（439 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.60 Å R-free 0.244
4EAD Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine Deposited 2012-03-22	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 2–440（439 aa）	Not recorded	0NP 2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine × 2 SO4 SULFATE ION × 12 GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions 273 K；COUNTER DIFFUSION, LIQUID DIFFUSION, temperature 273K	Resolution 1.50 Å R-free 0.192
4EAF Thymidine phosphorylase from E.coli Deposited 2012-03-22	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 2–440（439 aa）	Not recorded	SO4 SULFATE ION × 14 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；273 K；COUNTER DIFFUSION, temperature 273K, LIQUID DIFFUSION	Resolution 1.55 Å R-free 0.207
4LHM Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine Deposited 2013-07-01	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 2–440（439 aa）	Not recorded	SO4 SULFATE ION × 14 GOL GLYCEROL × 4 AZZ 3'-azido-3'-deoxythymidine × 2	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；298 K；COUNTER DIFFUSION, temperature 298.0K	Resolution 1.52 Å R-free 0.196

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

View Construct and Data Evidence

UniProt name	TYPH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–440； UniProt 2–440 Author chain B； PDBConstruct 2–440； UniProt 2–440

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1azy
Deposition date deposition_date	1997-11-24
Structure title title	STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE
Keywords keywords	GLYCOSYLTRANSFERASE, THYMIDINE PHOSPHORYLASE, SALVAGE PATHWAY; GLYCOSYLTRANSFERASE
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	37.40 Å
Radius of gyration Rg (electron density) rg_electron	37.36 Å
Forward intensity I(0) i0	137693000.00
Molecular weight molecular_weight	94356.0 kDa
Excluded volume excluded_volume	118020 Å³
Envelope volume envelope_volume	153870 Å³
Hydration-shell volume shell_volume	36633 Å³
Envelope diameter envelope_diameter	122.8 Å
Shell Rg shell_rg	41.13 Å
Envelope Rg envelope_rg	36.72 Å
Shape Rg shape_rg	37.39 Å
Total Rg total_rg	37.51 Å
Total atoms total_atoms	6612
Residues n_residues	880
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	122.4 Å
Rg (real space) rg_real	37.73 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	1.3770e+08
I(0) uncertainty (real space) i0_real_error	2.6210e+06
Rg (reciprocal space) rg_reciprocal	37.53 Å
I(0) (reciprocal space) i0_reciprocal	137700000.0000
Solution quality estimate total_estimate	0.7511
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.404
Kurtosis Kurtosis kurtosis	-0.812
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20400000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.763; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1azya1
Class class	a — All alpha proteins
Fold Fold fold	a.46 — Methionine synthase domain-like
Superfamily Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

Domain ID domain_id	d1azya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Superfamily Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Family Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	d1azya3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
Family Family family	d.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain

Domain ID domain_id	d1azya4
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	d1azyb1
Class class	a — All alpha proteins
Fold Fold fold	a.46 — Methionine synthase domain-like
Superfamily Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

Domain ID domain_id	d1azyb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Superfamily Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Family Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	d1azyb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
Family Family family	d.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain

Domain ID domain_id	d1azyb4
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 (6 domains)

Domain ID domain_id	1azyA01
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	1azyA02
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	1azyA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

Domain ID domain_id	1azyB01
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	1azyB02
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	1azyB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

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8. Citations (2)

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Unit-cell length a length_a	52.000 Å
Unit-cell length b length_b	78.000 Å
Unit-cell length c length_c	116.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2760

Description description	THYMIDINE PHOSPHORYLASE
Molecular weight formula_weight	47241.0 kDa
EC 编号 ec_number	2.4.2.4
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6612

STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE

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

THYMIDINE PHOSPHORYLASE

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/az/1azy/1azy.fit
pddf	/app/data/pr_computation/az/1azy/1azy.pr.out
profile	/app/data/saxs_computation/az/1azy/1azy.dat