1kdl

Solution structure of the amphipathic domain of YopD from Yersinia

Method: SOLUTION NMR
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1. Protein Identity and Related Structures Protein Identity & Related Structures

YOPD protein

OrganismNot specified

UniProt Q06131

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name YOPD_YERPS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–23; UniProt 278–300

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_id1kdl
Deposition date deposition_date2001-11-13
Structure title titleSolution structure of the amphipathic domain of YopD from Yersinia
Keywords keywordsYERSINIA, YOPD, AMPHIPATHIC ALPHA HELIX, BETA TURN, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodSOLUTION NMR
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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.

1kdl__assembly_1__model_1

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

Download this curve (.dat)

1kdl__assembly_1__model_1 | I(q)

10-2 10-1 104 105 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1kdl__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)11.80 Å
Rg (electron density)10.76 Å
Total Rg12.06 Å
Atom count387
Residues23
Excluded volume3433 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1kdl__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 (1)

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kdla_
Class classj — Peptides
Fold Fold foldj.35 — Transmembrane helical fragments
Superfamily Superfamily superfamilyj.35.1 — Transmembrane helical fragments
Family Family familyj.35.1.1 — Transmembrane helical fragments
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7. Citations (1)