1vf8

The Crystal Structure of Ym1 at 1.31 A Resolution

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

secretory protein

OrganismNot specified

UniProt O35744

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CH3L3_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–377; UniProt 22–398

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_id1vf8
Deposition date deposition_date2004-04-09
Structure title titleThe Crystal Structure of Ym1 at 1.31 A Resolution
Keywords keywordsYm1, chitinase, chi-lectin, structural plasticity, functional versatility, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

1vf8__assembly_1__model_1

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

Download this curve (.dat)

1vf8__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1vf8__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)21.36 Å
Rg (electron density)20.15 Å
Total Rg21.11 Å
Atom count2957
Residues373
Excluded volume52472 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1vf8__assembly_1__model_1 monomeric (1) 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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1vf8a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.5 — Type II chitinase
Domain ID domain_idd1vf8a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.26 — FKBP-like
Superfamily Superfamily superfamilyd.26.3 — Chitinase insertion domain
Family Family familyd.26.3.1 — Chitinase insertion domain

CATH v4.4 (2 domains)

Domain ID domain_id1vf8A01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1vf8A02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily10 —
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7. Citations (1)