6D3X: Plasminogen

Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma. Determined by X-ray diffraction at 1.8 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Helianthus annuus
Chains: 4
Atoms: 4,281
Mol. weight: 57.25 kDa
Released: 23 Jan 2019

Explore 6D3X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D3X contains 22 α-helices and 44 β-strands across 4 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: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	554-558	5
β-strand	563	1	1
β-strand	566-567	2	2
α-helix	568-569	2
β-strand	576-581	6	3
β-strand	586-594	9	3
β-strand	597-600	4	3
α-helix	602-605	4
α-helix	611-613	3
β-strand	614-618	5	3
β-strand	622	1	4
β-strand	631-640	10	3
β-strand	648-652	5	3
α-helix	655-658	4
β-strand	659	1	5
β-strand	662	1	5
α-helix	664-665	2
β-strand	666	1	2
α-helix	667-669	3
α-helix	674-675	2
β-strand	679-684	6	2
β-strand	696	1	4
β-strand	698-705	8	2
α-helix	707-710	4
β-strand	724-727	4	2
β-strand	735	1	1
β-strand	744-749	6	2
β-strand	752-763	12	2
β-strand	772-776	5	2
α-helix	777-780	4
α-helix	781-790	10

Chain B: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	554-558	5
β-strand	563	1	6
β-strand	566-567	2	7
α-helix	568-569	2
β-strand	576-580	5	8
β-strand	586-594	9	8
β-strand	597-600	4	8
α-helix	602-605	4
α-helix	611-613	3
β-strand	615-618	4	8
β-strand	622	1	9
β-strand	631-640	10	8
β-strand	648-652	5	8
α-helix	655-658	4
β-strand	659	1	10
β-strand	662	1	10
α-helix	664-665	2
β-strand	666	1	7
α-helix	667-669	3
α-helix	674-675	2
β-strand	679-684	6	7
β-strand	696	1	9
β-strand	698-705	8	7
α-helix	707-710	4
β-strand	724-727	4	7
β-strand	735	1	6
β-strand	744-749	6	7
β-strand	752-763	12	7
β-strand	772-776	5	7
α-helix	777-780	4
α-helix	781-789	9

Chains C and D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-11	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen	A, B	protein	246	Homo sapiens	P00747 (AlphaFold model)
Trypsin inhibitor 1	C, D	protein	14	Helianthus annuus	Q4GWU5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6D3X_1 Plasminogen (chains A, B)
FDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCL
EKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPA
CLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTEL
CAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIE
GVMRNN

Sequence of entity 2 (C, D), FASTA

>6D3X_2 Trypsin inhibitor 1 (chains C, D)
GRCYKSKPPICFPD

Primary citation

Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma. Swedberg, J.E., Wu, G., Mahatmanto, T. et al. J Med Chem (2019) 62:552-560. DOI 10.1021/acs.jmedchem.8b01139 · 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

Browse structure collections

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