← Back to search
3qv6

Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80.

Method: X-RAY DIFFRACTION
▼

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

Pyruvate kinase

Leishmania mexicana

UniProt Q27686

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 3-({4-[(2,4-dimethyl-5-sulfophenyl)amino]-9,10-dioxo-9,10-dihydroanthracen-1-yl}amino)-2,4,6-trimethylbenzenesulfonic acid × 4 POTASSIUM ION × 8 PHOSPHATE ION × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp 3hqp

16 assemblies; showing the first 12

Homodimer
3hqo 3hqo 3hqo 3hqo

4 assemblies

Homotetramer
1pkl 1pkl 3e0v 3e0v 3e0w 3hqn 3hqq 3hqq 3hqq 3hqq 3hqq 3hqq

19 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name KPYK_LEIME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–499； UniProt 1–499 Author chain D； PDBConstruct 1–499； UniProt 1–499

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3qv6
Deposition date deposition_date2011-02-25
Structure title titleCrystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80.
Keywords keywordsPyruvate kinase, glycolysis, tim barrel, sugar kinase, ADP/ATP binding, cytosol, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3qv6__assembly_1__model_1

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

Download this curve (.dat)

3qv6__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.

3qv6__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）41.92 Å
Rg (electron density)41.40 Å
Total Rg41.56 Å
Atom count13690
Residues1774
Excluded volume243790 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3qv6__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3qv6a1
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_idd3qv6a2
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_idd3qv6a3
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_idd3qv6d1
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_idd3qv6d2
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 (5 domains)

Domain ID domain_id3qv6A01
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_id3qv6A02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
Domain ID domain_id3qv6A03
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_id3qv6D01
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_id3qv6D02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily60 — Phosphoenolpyruvate-binding domains
▶

7. Citations (1)