6OQJ: Plasminogen kringle 2

Solution structure of the complex of mutant VEK50[RH1/AA] and plasminogen kringle 2. Determined by solution NMR. Released 24 Jul 2019.

Method: Solution NMR
Organisms: Homo sapiens, Streptococcus pyogenes
Chains: 2
Atoms: 1,133
Mol. weight: 16.19 kDa
Released: 24 Jul 2019

Explore 6OQJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OQJ contains 6 α-helices and 9 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	1
β-strand	22	1	2
α-helix	27	1
β-strand	28	1	2
β-strand	29	1	3
α-helix	30-31	2
α-helix	44-46	3
α-helix	48-50	3
β-strand	58	1	4
β-strand	67-69	3	4
β-strand	70	1	3
β-strand	77-79	3	4
β-strand	84	1	1

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	107-120	14
α-helix	125-149	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen kringle 2	A	protein	87	Homo sapiens	P00747 (AlphaFold model)
Plasminogen-binding group A streptococcal M-like protein PAM	B	protein	52	Streptococcus pyogenes	P49054 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6OQJ_1 Plasminogen kringle 2 (chains A)
YVEFSEECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNP
DRDLRPWCFTTDPNKRWEYCDIPRCAA

Sequence of entity 2 (B), FASTA

>6OQJ_2 Plasminogen-binding group A streptococcal M-like protein PAM (chains B)
GSVEKLTADAELQRLKNEAAEEAELERLKSERHDHDKKEAERKALEDKLADY

Primary citation

Solution structural model of the complex of the binding regions of human plasminogen with its M-protein receptor from Streptococcus pyogenes. Yuan, Y., Ayinuola, Y.A., Singh, D. et al. J Struct Biol (2019) 208:18-29. DOI 10.1016/j.jsb.2019.07.005 · PubMed

Other PDB entries of the same protein (UniProt P00747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5UGG 1.2 Å, Protease Inhibitor
6D3Y 1.32 Å, Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin…
5UGD 1.38 Å, Protease Inhibitor
6D40 1.43 Å, Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin…
8F7U 1.47 Å, Macrocyclic Plasmin Inhibitor
7UAH 1.57 Å, Macrocyclic plasmin inhibitor
8F7V 1.65 Å, Macrocyclic plasmin inhibitor
5HPG 1.66 Å, Structure and ligand determinants of the recombinant kringle 5 domain of human plasminogen
1KRN 1.67 Å, Structure of kringle 4 at 4C temperature and 1.67 Å resolution
6OG4 1.7 Å, plasminogen binding group A streptococcal M protein
1KI0 1.75 Å, The X-ray Structure of Human Angiostatin
4CIK 1.78 Å, plasminogen kringle 1 in complex with inhibitor

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