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6nn8

The structure of human liver pyruvate kinase, hLPYK-S531E

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

Pyruvate kinase PKLR

Homo sapiens

UniProt P30613

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 1,2-ETHANEDIOL × 24 water × 4 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 4 1,2-ETHANEDIOL × 17 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
9rdf 9rdf

2 assemblies

Homotetramer
2vgb 2vgf 2vgg 2vgi 4ip7 6nn4 6nn5 6nn7 6nn7 6nn8 6nn8 7frv

70 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name KPYR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–543； UniProt 34–574 Author chain B； PDBConstruct 3–543； UniProt 34–574 Author chain C； PDBConstruct 3–543； UniProt 34–574 Author chain D； PDBConstruct 3–543； UniProt 34–574 Author chain E； PDBConstruct 3–543； UniProt 34–574 Author chain F； PDBConstruct 3–543； UniProt 34–574 Author chain G； PDBConstruct 3–543； UniProt 34–574 Author chain H； PDBConstruct 3–543； UniProt 34–574

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_id6nn8
Deposition date deposition_date2019-01-14
Structure title titleThe structure of human liver pyruvate kinase, hLPYK-S531E
Keywords keywordspyruvate kinase, allosteric, glycolysis, 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.

6nn8__assembly_1__model_1

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

Download this curve (.dat)

6nn8__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.

6nn8__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）38.77 Å
Rg (electron density)38.16 Å
Total Rg38.47 Å
Atom count28687
Residues1851
Excluded volume253520 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6nn8__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6nn8__assembly_2__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 (3)

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id6nn8A01
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_id6nn8A02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8B01
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_id6nn8B02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8C01
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_id6nn8C02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8D01
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_id6nn8D02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8E01
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_id6nn8E02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8F01
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_id6nn8F02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8G01
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_id6nn8G02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id6nn8H01
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_id6nn8H02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
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7. Citations (1)