7THS: Macrocyclic plasmin inhibitor

Macrocyclic plasmin inhibitor. Determined by X-ray diffraction at 1.8 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,289
Mol. weight: 57.02 kDa
Ligands: I5Y, I5Q
Released: 18 Jan 2023

Explore 7THS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7THS contains 22 α-helices and 40 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
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	752-761	10	2
β-strand	772-776	5	2
α-helix	777-779	3
α-helix	781-790	10

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	554-555	2
α-helix	557-558	2
β-strand	563	1	6
β-strand	566-567	2	7
α-helix	568-569	2
β-strand	576-581	6	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	614-618	5	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	752-761	10	7
β-strand	772-776	5	7
α-helix	777-780	4
α-helix	781-789	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen	A, B	protein	250	Homo sapiens	P00747 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7THS_1 Plasminogen (chains A, B)
AAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTA
AHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDK
VIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQ
STELCAGHLAGGTDSCQGDAGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFV
TWIEGVMRNN

Ligands and cofactors

ID	Name	Formula	Copies
I5Y	(6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3…	C43 H52 N8 O6 S	2
I5Q	(2S)-butane-1,2-diol	C4 H10 O2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Synthesis and Structural Characterization of Macrocyclic Plasmin Inhibitors. Wiedemeyer, S.J.A., Wu, G., Pham, T.L.P. et al. ChemMedChem (2023) 18:e202200632-e202200632. DOI 10.1002/cmdc.202200632 · 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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