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2vgi

HUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT

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

PYRUVATE KINASE ISOZYMES R/L

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 1,6-di-O-phosphono-beta-D-fructofuranose × 4 2-PHOSPHOGLYCOLIC ACID × 4 POTASSIUM ION × 4 MANGANESE (II) ION × 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 1–528； UniProt 47–574 Author chain B； PDBConstruct 1–528； UniProt 47–574 Author chain C； PDBConstruct 1–528； UniProt 47–574 Author chain D； PDBConstruct 1–528； UniProt 47–574

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_id2vgi
Deposition date deposition_date2007-11-13
Structure title titleHUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT
Keywords keywordsGLYCOLYSIS, 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.

2vgi__assembly_1__model_1

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

Download this curve (.dat)

2vgi__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.

2vgi__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）41.05 Å
Rg (electron density)40.73 Å
Total Rg40.93 Å
Atom count15342
Residues2008
Excluded volume273810 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2vgi__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 (5)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd2vgia1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.1 — Pyruvate kinase beta-barrel domain
Domain ID domain_idd2vgia2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family familyc.1.12.1 — Pyruvate kinase
Domain ID domain_idd2vgia3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamilyc.49.1 — PK C-terminal domain-like
Family Family familyc.49.1.1 — Pyruvate kinase, C-terminal domain
Domain ID domain_idd2vgib1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.1 — Pyruvate kinase beta-barrel domain
Domain ID domain_idd2vgib2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family familyc.1.12.1 — Pyruvate kinase
Domain ID domain_idd2vgib3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamilyc.49.1 — PK C-terminal domain-like
Family Family familyc.49.1.1 — Pyruvate kinase, C-terminal domain
Domain ID domain_idd2vgic1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.1 — Pyruvate kinase beta-barrel domain
Domain ID domain_idd2vgic2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family familyc.1.12.1 — Pyruvate kinase
Domain ID domain_idd2vgic3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamilyc.49.1 — PK C-terminal domain-like
Family Family familyc.49.1.1 — Pyruvate kinase, C-terminal domain
Domain ID domain_idd2vgid1
Class classb — All beta proteins
Fold Fold foldb.58 — PK beta-barrel domain-like
Superfamily Superfamily superfamilyb.58.1 — PK beta-barrel domain-like
Family Family familyb.58.1.1 — Pyruvate kinase beta-barrel domain
Domain ID domain_idd2vgid2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family familyc.1.12.1 — Pyruvate kinase
Domain ID domain_idd2vgid3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.49 — Pyruvate kinase C-terminal domain-like
Superfamily Superfamily superfamilyc.49.1 — PK C-terminal domain-like
Family Family familyc.49.1.1 — Pyruvate kinase, C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id2vgiA01
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_id2vgiA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id2vgiA03
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_id2vgiB01
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_id2vgiB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id2vgiB03
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_id2vgiC01
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_id2vgiC02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id2vgiC03
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_id2vgiD01
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_id2vgiD02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id2vgiD03
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)