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9vak

Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex

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

Lacto-N-biosidase

Bifidobacterium bifidum JCM 1254

UniProt B3TLD6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 其他Polymer 1 beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1 Consistent with protein count
2 Other combination Monomer Protein 1 其他Polymer 1 beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1 Consistent with protein count
3 Other combination Monomer Protein 1 其他Polymer 1 beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1 Consistent with protein count
4 Other combination Monomer Protein 1 其他Polymer 1 beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4jaw 4jaw 5bxr 5bxr 5bxs 5bxs 5bxt 5bxt 9wfh 9wfh

10 assemblies

Homodimer
4jaw

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4h04 4h04 4h04 5bxp 5bxp 9vak 9vak 9vak 9vak

9 assemblies

View Construct and Data Evidence
UniProt name LNBB_BIFB1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–183； UniProt 775–938 Author chain B； PDBConstruct 20–183； UniProt 775–938 Author chain C； PDBConstruct 20–183； UniProt 775–938 Author chain D； PDBConstruct 20–183； UniProt 775–938

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_id9vak
Deposition date deposition_date2025-06-03
Structure title titleCarbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex
Keywords keywordsCarbohydrate Binding Module Family 32 domain, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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.

9vak__assembly_3__model_1

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

Download this curve (.dat)

9vak__assembly_3__model_1 | I(q)

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

9vak__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）16.63 Å
Rg (electron density)15.30 Å
Total Rg16.48 Å
Atom count1245
Residues162
Excluded volume21915 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9vak__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9vak__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9vak__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9vak__assembly_4__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 (4)

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7. Citations (2)