SAXSdb — 1a3x

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

PYRUVATE KINASE

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–500 Chain B； UniProt 1–500	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 4 MN MANGANESE (II) ION × 4 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；28-33% (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE PH 6.5	Resolution 3.00 Å R-free 0.341
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–500 Chain B； UniProt 1–500	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 2 MN MANGANESE (II) ION × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；28-33% (W/V) PEG 8000, 200 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE PH 6.5	Resolution 3.00 Å R-free 0.341

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 1A3X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A3W PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+ Deposited 1998-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–500（500 aa） Chain B 1–500（500 aa）	Not recorded	PGA 2-PHOSPHOGLYCOLIC ACID × 4 FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 4 MN MANGANESE (II) ION × 4 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å R-free 0.323

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KPYK1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–500； UniProt 1–500 Author chain B； PDBConstruct 1–500； UniProt 1–500

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	1a3x
Deposition date deposition_date	1998-01-26
Structure title title	PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+
Keywords keywords	PYRUVATE KINASE, ALLOSTERIC REGULATION, TRANSFERASE; TRANSFERASE
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	45.85 Å
Radius of gyration Rg (electron density) rg_electron	46.11 Å
Forward intensity I(0) i0	164017000.00
Molecular weight molecular_weight	106680.0 kDa
Excluded volume excluded_volume	134030 Å³
Envelope volume envelope_volume	190880 Å³
Hydration-shell volume shell_volume	34194 Å³
Envelope diameter envelope_diameter	150.7 Å
Shell Rg shell_rg	51.83 Å
Envelope Rg envelope_rg	44.73 Å
Shape Rg shape_rg	46.09 Å
Total Rg total_rg	46.42 Å
Total atoms total_atoms	7472
Residues n_residues	974
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	154.2 Å
Rg (real space) rg_real	46.27 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	1.6400e+08
I(0) uncertainty (real space) i0_real_error	3.3210e+06
Rg (reciprocal space) rg_reciprocal	45.85 Å
I(0) (reciprocal space) i0_reciprocal	163900000.0000
Solution quality estimate total_estimate	0.6809
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.260
Kurtosis Kurtosis kurtosis	-1.070
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18040000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.193; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.390; Smooth: 0.877

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PYRUVATE KINASE
Molecular weight formula_weight	54612.4 kDa
EC 编号 ec_number	2.7.1.40
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7472

MSRLERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGLNIVRMNFSHGSYEYHKSVIDNARKSEELYPGRPLAIALDTKGPEIRTGTTTNDVDYPIPPNHEMIFTTDDKYAKACDDKIMYVDYKNITKVISAGRIIYVDDGVLSFQVLEVVDDKTLKVKALNAGKICSHKGVNLPGTDVDLPALSEKDKEDLRFGVKNGVHMVFASFIRTANDVLTIREVLGEQGKDVKIIVKIENQQGVNNFDEILKVTDGVMVARGDLGIEIPAPEVLAVQKKLIAKSNLAGKPVICATQMLESMTYNPRPTRAEVSDVGNAILDGADCVMLSGETAKGNYPINAVTTMAETAVIAEQAIAYLPNYDDMRNCTPKPTSTTETVAASAVAAVFEQKAKAIIVLSTSGTTPRLVSKYRPNCPIILVTRCPRAARFSHLYRGVFPFVFEKEPVSDWTDDVEARINFGIEKAKEFGILKKGDTYVSIQGFKAGAGHSNTLQVSTV

Entity 2 Entity 2 non-polymer

Description description	2-PHOSPHOGLYCOLIC ACID
Molecular weight formula_weight	156.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1a3xa1
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d1a3xa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d1a3xa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	d1a3xb1
Class class	b — All beta proteins
Fold Fold fold	b.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamily	b.58.1 — PK beta-barrel domain-like
Family Family family	b.58.1.1 — Pyruvate kinase beta-barrel domain

Domain ID domain_id	d1a3xb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.1 — Pyruvate kinase

Domain ID domain_id	d1a3xb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamily	c.49.1 — PK C-terminal domain-like
Family Family family	c.49.1.1 — Pyruvate kinase, C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1a3xA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	1a3xA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	1a3xA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

Domain ID domain_id	1a3xB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily	20 — Pyruvate kinase, C-terminal domain

Domain ID domain_id	1a3xB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	1a3xB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily	10 — PK beta-barrel domain-like

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8. Citations (1)

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Unit-cell length a length_a	108.300 Å
Unit-cell length b length_b	106.400 Å
Unit-cell length c length_c	105.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.80 °
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	3.000 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.3410

fit	/app/data/saxs_computation/a3/1a3x/1a3x.fit
pddf	/app/data/pr_computation/a3/1a3x/1a3x.pr.out
profile	/app/data/saxs_computation/a3/1a3x/1a3x.dat

PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+

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

PYRUVATE KINASE

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