Plasminogen-binding group A streptococcal M-like protein PAM
Streptococcus pyogenes
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 85–133 | Fragment：residues 85-133 | No other associated polymer | SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N] VEK50, 2 ug/mL DSS, 20 mM [U-2H] Bis-Tris-d19, 1 ug/mL DTT, 1 ug/mL sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O | 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 6OKW | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1I5K STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 DOMAIN OF HUMAN PLASMINOGEN TO AN INTERNAL PEPTIDE FROM A GROUP A STREPTOCOCCAL SURFACE PROTEIN Deposited 2001-02-27 | 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 C
85–113（29 aa）
Fragment：VEK-30 (30 RESIDUE INTERNAL PEPTIDE)
Chain D
85–113（29 aa）
Fragment：VEK-30 (30 RESIDUE INTERNAL PEPTIDE)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；23%(w/v) PEG 3350, 0.1 M Mes, 0.2 M Li2SO4, 2mM CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.70 Å R-free 0.262 |
| 2DOI The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM Deposited 2006-04-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
85–113（29 aa）
Fragment：VEK-30
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.296 |
| 2DOI The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM Deposited 2006-04-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
85–113（29 aa）
Fragment：VEK-30
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.10 Å R-free 0.296 |
| 6OG4 plasminogen binding group A streptococcal M protein Deposited 2019-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
76–150（75 aa）
Fragment：UNP residues 76-150
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES, pH 7.0, 2 M ammonium sulfate
|
Resolution 1.70 Å R-free 0.220 |
| 6OKX Solution structure of VEK50RH1/AA Deposited 2019-04-15 | Different mutation/modification Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
85–133（49 aa）
Fragment：residues 85-133
|
Mutation：R101A, H102A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
0.5 mM [U-99% 13C; U-99% 15N] VEK50RH1/AA, 2 ug/mL DSS, 1 ug/mL DTT, 20 mM [U-2H] Bis-Tris-d19, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 6OKY Solution structure of truncated peptide from PAMap53 Deposited 2019-04-15 | Different mutation/modification Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
85–133（49 aa）
Fragment：residues 85-133
|
Mutation：R114A, H115A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
0.5 mM [U-99% 13C; U-99% 15N] Truncated peptide from PAMAP53, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 1 ug/mL sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 6OQ9 Solution structure of VEK50 in the bound form with plasminogen kringle 2 Deposited 2019-04-25 | Different experimental conditions | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
85–133（49 aa）
Fragment：residues 85-133
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
0.5 mM [U-99% 13C; U-99% 15N] VEK50, 1.5 mM Kringle 2, 2 ug/mL DSS, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL sodium azide, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 6OQJ SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH1/AA] AND PLASMINOGEN KRINGLE 2 Deposited 2019-04-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
85–133（49 aa）
Fragment：residues 85-134
|
Mutation：R19A, H20A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
1.0 mM [U-99% 13C; U-99% 15N] plasminogen kringle 2, 1.0 mM VEK50[RH1/AA], 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1 mM [U-99% 13C; U-99% 15N] VEK50[RH1/AA], 1 mM plasminogen kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6OQK SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH2/AA] AND PLASMINOGEN KRINGLE 2 Deposited 2019-04-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
85–133（49 aa）
|
Mutation：R32A, H33A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
1.0 mM [U-99% 13C; U-99% 15N] plasminogen Kringle 2, 1.0 mM VEK50[RH2/AA], 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.0 mM [U-99% 13C; U-99% 15N] VEK50[RH2/AA], 1.0 mM plasminogen Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 8TVL Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen Deposited 2023-08-18 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
30–385（356 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PAM_STRPY |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 3–51； UniProt 85–133 |
