SAXSdb — 6oqk

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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 85–133	Mutation：R32A, H33A	Plasminogen Kringle 2 × 1	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

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 6OQK	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 mutation/modification 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 mutation/modification 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 mutation/modification 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
6OKW Solution structure of VEK50 Deposited 2019-04-15	Different construct Different mutation/modification Different oligomeric state 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, 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
6OKX Solution structure of VEK50RH1/AA Deposited 2019-04-15	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 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
8TVL Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen Deposited 2023-08-18	Different construct Different mutation/modification Different oligomeric state 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–51； UniProt 85–133

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_id	6oqk
Deposition date deposition_date	2019-04-26
Structure title title	SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH2/AA] AND PLASMINOGEN KRINGLE 2
Keywords keywords	Plasminogen binding peptide, blood clotting, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.15 Å
Radius of gyration Rg (electron density) rg_electron	18.16 Å
Forward intensity I(0) i0	433559000.00
Molecular weight molecular_weight	161540.0 kDa
Excluded volume excluded_volume	196820 Å³
Envelope volume envelope_volume	53735 Å³
Hydration-shell volume shell_volume	20779 Å³
Envelope diameter envelope_diameter	82.7 Å
Shell Rg shell_rg	28.68 Å
Envelope Rg envelope_rg	23.77 Å
Shape Rg shape_rg	18.15 Å
Total Rg total_rg	18.57 Å
Total atoms total_atoms	22030
Residues n_residues	1390
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	47.6 Å
Rg (real space) rg_real	17.23 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	4.1290e+08
I(0) uncertainty (real space) i0_real_error	3.5520e+06
Rg (reciprocal space) rg_reciprocal	18.27 Å
I(0) (reciprocal space) i0_reciprocal	433600000.0000
Solution quality estimate total_estimate	0.6848
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.517
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	4.2070
Highest regularization parameter α highest_alpha	478600.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.997; Stabil: 0.974; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Plasminogen Kringle 2
Molecular weight formula_weight	10166.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	22030

YVEFSEECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRCAA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	Plasminogen-binding group A streptococcal M-like protein PAM
Molecular weight formula_weight	6020.6 kDa
Mutation mutation	R32A, H33A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSVEKLTADAELQRLKNERHEEAELERLKSEAADHDKKEAERKALEDKLADY

来源 Source

来源生物 organism	Streptococcus pyogenes
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6oqka1
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.0 — automated matches

Domain ID domain_id	d6oqka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6oqkA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

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8. Citations (1)

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fit	/app/data/saxs_computation/oq/6oqk/6oqk.fit
pddf	/app/data/pr_computation/oq/6oqk/6oqk.pr.out
profile	/app/data/saxs_computation/oq/6oqk/6oqk.dat

SOLUTION STRUCTURE OF THE COMPLEX OF MUTANT VEK50[RH2/AA] AND PLASMINOGEN KRINGLE 2

1. Protein Identity and Related Structures Protein Identity & Related Structures

Plasminogen-binding group A streptococcal M-like protein PAM

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)