1BML: Plasmin

Complex of the catalytic domain of human plasmin and streptokinase. Determined by X-ray diffraction at 2.9 Å resolution. Released 2 Aug 1999.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Streptococcus dysgalactiae subsp. equisimilis
Chains: 4
Atoms: 8,940
Mol. weight: 136.96 kDa
Released: 2 Aug 1999

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

Secondary structure: helices and β-sheets

1BML contains 32 α-helices and 95 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, 22 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	588-594	7	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	626	1	5
α-helix	627	1
β-strand	631-633	3	3
β-strand	635-640	6	3
β-strand	648-652	5	3
β-strand	659	1	6
β-strand	662	1	6
α-helix	664-665	2
β-strand	666	1	2
α-helix	667-669	3
β-strand	679-684	6	2
β-strand	696	1	4
α-helix	697	1
β-strand	698-705	8	2
α-helix	707-710	4
β-strand	724-727	4	2
β-strand	735	1	1
β-strand	744-748	5	2
β-strand	753-761	9	2
β-strand	772-776	5	2
α-helix	781-788	8

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	563	1	7
β-strand	566-567	2	8
α-helix	568-569	2
β-strand	577-580	4	9
β-strand	586-590	5	9
β-strand	591-594	4	10
β-strand	597-600	4	10
α-helix	602-605	4
α-helix	611-613	3
β-strand	615-618	4	9
β-strand	622	1	11
β-strand	626	1	12
α-helix	627	1
β-strand	631-634	4	9
β-strand	635-640	6	10
β-strand	648-652	5	10
β-strand	659	1	13
β-strand	662	1	13
α-helix	664-665	2
β-strand	666	1	8
α-helix	667	1
β-strand	679-684	6	8
β-strand	696	1	11
β-strand	698-705	8	8
α-helix	707-710	4
β-strand	724-727	4	8
β-strand	735	1	7
β-strand	744-748	5	8
β-strand	753-761	9	8
β-strand	772-776	5	8
α-helix	778-780	3
α-helix	781-788	8

Chain C: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17-26	10	14
β-strand	32-33	2	14
β-strand	39-41	3	14
β-strand	72-75	4	15
α-helix	76-87	12
α-helix	94-96	3
β-strand	98-103	6	14
β-strand	108-110	3	14
β-strand	116-117	2	14
β-strand	124-127	4	15
β-strand	135-145	11	14
α-helix	148-150	3
β-strand	154	1	16
β-strand	158-168	11	17
β-strand	183-188	6	17
β-strand	194-195	2	18
α-helix	196-209	14
β-strand	215-226	12	17
α-helix	232	1
β-strand	233-234	2	17
α-helix	235	1
β-strand	242-243	2	18
β-strand	249	1	16
α-helix	264-265	2
β-strand	266-277	12	17
β-strand	293-301	9	5
β-strand	307-315	9	5
α-helix	318-320	3
β-strand	323	1	19
β-strand	336	1	19
α-helix	341-343	3
β-strand	348-356	9	5
β-strand	363-371	9	5

Chain D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	20
β-strand	23-26	4	21
β-strand	32-34	3	21
β-strand	38-41	4	20
β-strand	72-75	4	22
α-helix	76-88	13
α-helix	94-96	3
β-strand	98-103	6	21
β-strand	108-110	3	20
β-strand	116-117	2	20
β-strand	124-127	4	22
β-strand	134-138	5	20
β-strand	140-145	6	21
β-strand	154	1	23
β-strand	158-168	11	24
β-strand	183-184	2	24
β-strand	194-195	2	25
α-helix	196-209	14
β-strand	215-226	12	24
β-strand	233-234	2	24
β-strand	242-243	2	25
β-strand	249	1	23
β-strand	266-277	12	24
β-strand	293-301	9	12
β-strand	307-315	9	12
β-strand	323	1	26
α-helix	329-331	3
β-strand	336	1	26
α-helix	341-343	3
β-strand	349-356	8	12
β-strand	364-370	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasmin	A, B	protein	250	Homo sapiens	P00747 (AlphaFold model)
Streptokinase	C, D	protein	362	Streptococcus dysgalactiae subsp. equisimilis	P00779 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1BML_1 PLASMIN (chains A, B)
AAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTA
AHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDK
VIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQ
STELCAGHLAGGTDSCQGDAGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFV
TWIEGVMRNN

Sequence of entity 2 (C, D), FASTA

>1BML_2 STREPTOKINASE (chains C, D)
SVNNSQLVVSVAGTVEGTNQDISLKFFEIDLTSRPAHGGKTEQGLSPKSKPFATDSGAMP
HKLEKADLLKAIQEQLIANVHSNDDYFEVIDFASDATITDRNGKVYFADKDGSVTLPTQP
VQEFLLSGHVRVRPYKEKPIQNQAKSVDVEYTVQFTPLNPDDDFRPGLKDTKLLKTLAIG
DTITSQELLAQAQSILNKTHPGYTIYERDSSIVTHDNDIFRTILPMDQEFTYHVKNREQA
YEINKKSGLNEEINNTDLISEKYYVLKKGEKPYDPFDRSHLKLFTIKYVDVNTNELLKSE
QLLTASERNLDFRDLYDPRDKAKLLYNNLDAFGIMDYTLTGKVEDNHDDTNRIITVYMGK
RP

Primary citation

Crystal structure of the catalytic domain of human plasmin complexed with streptokinase. Wang, X., Lin, X., Loy, J.A. et al. Science (1998) 281:1662-1665. DOI 10.1126/science.281.5383.1662 · 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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1BML is part of these collections:

Blood clotting

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