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3srf

Human M1 pyruvate kinase

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

Pyruvate kinase isozymes M1/M2

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 PHOSPHATE ION × 4 POTASSIUM ION × 4 MAGNESIUM ION × 4 PYRUVIC ACID × 4 GLYCEROL × 6 water × 4 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 4 PHOSPHATE ION × 4 POTASSIUM ION × 4 MAGNESIUM ION × 4 PYRUVIC ACID × 4 GLYCEROL × 3 water × 4 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 4 PHOSPHATE ION × 4 POTASSIUM ION × 4 MAGNESIUM ION × 4 PYRUVIC ACID × 4 GLYCEROL × 4 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 21–551； UniProt 1–531 Author chain B； PDBConstruct 21–551； UniProt 1–531 Author chain C； PDBConstruct 21–551； UniProt 1–531 Author chain D； PDBConstruct 21–551； UniProt 1–531 Author chain E； PDBConstruct 21–551； UniProt 1–531 Author chain F； PDBConstruct 21–551； UniProt 1–531 Author chain G； PDBConstruct 21–551； UniProt 1–531 Author chain H； PDBConstruct 21–551； UniProt 1–531

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_id3srf
Deposition date deposition_date2011-07-07
Structure title titleHuman M1 pyruvate kinase
Keywords keywordsTIM Barrel, Phosphoryl transfer, PEP Binding, cytosol, 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.

3srf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3srf__assembly_3__model_1 | I(q)

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

3srf__assembly_3__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）40.95 Å
Rg (electron density)40.88 Å
Total Rg41.17 Å
Atom count15944
Residues2068
Excluded volume285310 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3srf__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3srf__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3srf__assembly_3__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 (7)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id3srfA01
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_id3srfA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfA03
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_id3srfB01
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_id3srfB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfB03
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_id3srfC01
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_id3srfC02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfC03
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_id3srfD01
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_id3srfD02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfD03
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_id3srfE01
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_id3srfE02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfE03
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_id3srfF01
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_id3srfF02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfF03
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_id3srfG01
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_id3srfG02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfG03
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_id3srfH01
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_id3srfH02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3srfH03
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)