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4yj5

Crystal structure of PKM2 mutant

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate kinase PKM

Homo sapiens

UniProt P14618

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 PYRUVIC ACID × 4 MAGNESIUM ION × 4 SERINE × 4 1,6-di-O-phosphono-beta-D-fructofuranose × 3 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3g2g 3g2g 6b6u 6nu1 6nu1 6nu1 6nu1 6nu5 6nub

9 assemblies

Homotetramer
1t5a 1t5a 1zjh 3bjf 3bjt 3g2g 3gqy 3gr4 3h6o 3me3 3srd 3srf

67 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name KPYM_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–518； UniProt 14–531 Author chain B； PDBConstruct 1–518； UniProt 14–531 Author chain C； PDBConstruct 1–518； UniProt 14–531 Author chain D； PDBConstruct 1–518； UniProt 14–531

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_id4yj5
Deposition date deposition_date2015-03-03
Structure title titleCrystal structure of PKM2 mutant
Keywords keywordsPKM2 mutant, TRANSFERASE; TRANSFERASE
Experimental Method methodX-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.

4yj5__assembly_1__model_1

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

Download this curve (.dat)

4yj5__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4yj5__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）41.19 Å
Rg (electron density)41.04 Å
Total Rg41.34 Å
Atom count15984
Residues2072
Excluded volume285760 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4yj5__assembly_1__model_1 tetrameric （4） 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)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id4yj5A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily20 — Pyruvate kinase, C-terminal domain
Domain ID domain_id4yj5A02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id4yj5A03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily10 — PK beta-barrel domain-like
Domain ID domain_id4yj5B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily20 — Pyruvate kinase, C-terminal domain
Domain ID domain_id4yj5B02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id4yj5B03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily10 — PK beta-barrel domain-like
Domain ID domain_id4yj5C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily20 — Pyruvate kinase, C-terminal domain
Domain ID domain_id4yj5C02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id4yj5C03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily10 — PK beta-barrel domain-like
Domain ID domain_id4yj5D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1380 — Pyruvate Kinase; Chain: A, domain 1
Homologous superfamily homologous superfamily20 — Pyruvate kinase, C-terminal domain
Domain ID domain_id4yj5D02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id4yj5D03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology33 — M1 Pyruvate Kinase; Domain 3
Homologous superfamily homologous superfamily10 — PK beta-barrel domain-like
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7. Citations (1)