1DDJ: Human plasminogen catalytic domain

Crystal structure of human plasminogen catalytic domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 18 Feb 2000.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,341
Mol. weight: 108.32 kDa
Released: 18 Feb 2000

Explore 1DDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DDJ contains 42 α-helices and 77 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	566-567	2	1
α-helix	568-569	2
β-strand	576-580	5	2
β-strand	586-594	9	2
β-strand	597-600	4	2
α-helix	602-605	4
α-helix	611-613	3
β-strand	615-618	4	2
β-strand	622	1	3
β-strand	631-640	10	2
β-strand	648-652	5	2
α-helix	664-665	2
β-strand	666	1	1
α-helix	674-675	2
β-strand	679-684	6	1
β-strand	696	1	3
β-strand	698-705	8	1
α-helix	707-710	4
β-strand	724-727	4	1
β-strand	736	1	4
β-strand	744-748	5	1
β-strand	753-759	7	1
α-helix	761-763	3
β-strand	766	1	4
β-strand	767	1	5
β-strand	770	1	5
β-strand	772-776	5	1
α-helix	777-779	3
α-helix	781-789	9

Chain B: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	566-567	2	6
α-helix	568-569	2
β-strand	576-580	5	7
β-strand	586-594	9	7
β-strand	597-600	4	7
α-helix	602-605	4
α-helix	611-613	3
β-strand	615-618	4	7
β-strand	622	1	8
β-strand	631-640	10	7
β-strand	648-652	5	7
α-helix	655-658	4
α-helix	664-665	2
β-strand	666	1	6
α-helix	667-669	3
α-helix	674-675	2
β-strand	679-684	6	6
β-strand	696	1	8
β-strand	698-705	8	6
α-helix	707-710	4
β-strand	724-727	4	6
β-strand	736	1	9
β-strand	744-748	5	6
β-strand	753-759	7	6
α-helix	761-763	3
β-strand	766	1	9
β-strand	772-776	5	6
α-helix	777-780	4
α-helix	781-790	10

Chain C: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	566-567	2	10
α-helix	568-569	2
β-strand	576-581	6	11
β-strand	586-594	9	11
β-strand	597-600	4	11
α-helix	602-605	4
α-helix	611-613	3
β-strand	614-618	5	11
β-strand	622	1	12
β-strand	631-640	10	11
β-strand	648-652	5	11
α-helix	664-665	2
β-strand	666	1	10
α-helix	668-669	2
α-helix	674-675	2
β-strand	679-684	6	10
β-strand	696	1	12
β-strand	698-705	8	10
α-helix	707-710	4
β-strand	724-727	4	10
β-strand	744-748	5	10
β-strand	753-759	7	10
α-helix	761-763	3
β-strand	767	1	13
β-strand	770	1	13
β-strand	772-776	5	10
α-helix	777-779	3
α-helix	781-790	10

Chain D: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	554-555	2
β-strand	566-567	2	14
α-helix	568-569	2
β-strand	576-581	6	15
β-strand	586-594	9	15
β-strand	597-600	4	15
α-helix	602-605	4
α-helix	611-613	3
β-strand	614-618	5	15
β-strand	622	1	16
β-strand	631-640	10	15
β-strand	648-652	5	15
α-helix	655-658	4
α-helix	664-665	2
β-strand	666	1	14
α-helix	668-669	2
α-helix	674-675	2
β-strand	679-684	6	14
β-strand	694	1	16
β-strand	696	1	16
β-strand	698-705	8	14
α-helix	707-710	4
β-strand	724-727	4	14
β-strand	736	1	17
β-strand	744-748	5	14
β-strand	753-759	7	14
α-helix	761-763	3
β-strand	766	1	17
β-strand	767	1	18
β-strand	770	1	18
β-strand	772-776	5	14
α-helix	777-779	3
α-helix	781-790	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen	A, B, C, D	protein	247	Homo sapiens	P00747 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1DDJ_1 PLASMINOGEN (chains A, B, C, D)
SFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHC
LEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIP
ACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTE
LCAGHLAGGTDSCQGDAGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWI
EGVMRNN

Primary citation

Human plasminogen catalytic domain undergoes an unusual conformational change upon activation. Wang, X., Terzyan, S., Tang, J. et al. J Mol Biol (2000) 295:903-914. DOI 10.1006/jmbi.1999.3397 · 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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