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2kk9

Anti-group A streptococcal vaccine epitope: structure, stability and its ability to interact with HLA class II molecules

Method: SOLUTION NMR Dmax: 64.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

M protein, serotype 5

OrganismNot specified

UniProt P02977

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 300–354 Fragment：UNP residues 300-354 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3.7；295 K；Pressure ambient NMR sample composition：5.4 mg/mL, trifluoroethanol/water 30/70% | trifluoroethanol/water 30/70% Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2KK9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MMU M5 protein with Factor H 6-7 domain Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 94–175（82 aa）
Chain B 94–175（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 6000, Ethylene glycol, Sodium Chloride
Resolution 2.25 Å R-free 0.287
9MMU M5 protein with Factor H 6-7 domain Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 94–175（82 aa）
Chain F 94–175（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 6000, Ethylene glycol, Sodium Chloride
Resolution 2.25 Å R-free 0.287

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name M5_STRP5
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–55； UniProt 300–354

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2kk9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2kk9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2kk9
Deposition date deposition_date2009-06-16
Structure title titleAnti-group A streptococcal vaccine epitope: structure, stability and its ability to interact with HLA class II molecules
Keywords keywords;S. pyogenes, M5 protein, Synthetic peptide vaccine, Cell wall, Peptidoglycan-anchor, Phagocytosis, Secreted, Virulence, UNKNOWN FUNCTION, ANTIMICROBIAL PROTEIN ;; ANTIMICROBIAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.40 Å
Radius of gyration Rg (electron density) rg_electron19.17 Å
Forward intensity I(0) i01026180.00
Molecular weight molecular_weight6367.0 kDa
Excluded volume excluded_volume7804 ų
Envelope volume envelope_volume13714 ų
Hydration-shell volume shell_volume6894 ų
Envelope diameter envelope_diameter63.5 Å
Shell Rg shell_rg22.67 Å
Envelope Rg envelope_rg18.82 Å
Shape Rg shape_rg19.11 Å
Total Rg total_rg20.08 Å
Total atoms total_atoms910
Residues n_residues55
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax64.6 Å
Rg (real space) rg_real19.64 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real1.0260e+06
I(0) uncertainty (real space) i0_real_error1.5070e+04
Rg (reciprocal space) rg_reciprocal19.61 Å
I(0) (reciprocal space) i0_reciprocal1026000.0000
Solution quality estimate total_estimate0.7351
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary12.7 Å
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.716
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha80490.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.740; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.334; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2kk9A00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily460 —
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8. Citations (1)

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9. Files and Curves (10)