4JK5: Human urokinase-type Plasminogen Activator

Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser). Determined by X-ray diffraction at 1.55 Å resolution. Released 17 Jul 2013.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Homo sapiens, Synthetic construct
Chains: 2
Atoms: 2,255
Mol. weight: 30.5 kDa
Ligands: ZBR
Released: 17 Jul 2013

Explore 4JK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JK5 contains 9 α-helices and 22 β-strands across 1 chain. 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	17	1	1
β-strand	20-21	2	2
α-helix	24-26	3
β-strand	30-36	7	3
β-strand	38-48	11	3
β-strand	51-54	4	3
α-helix	56-58	3
α-helix	62-63	3
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-90	10	3
β-strand	95-96	2	5
β-strand	99-100	2	5
β-strand	104-109	6	3
β-strand	122	1	2
α-helix	123-125	3
α-helix	130-131	2
β-strand	135-140	6	2
β-strand	154	1	4
β-strand	156-163	8	2
α-helix	165-168	4
α-helix	173-175	3
β-strand	180-184	5	2
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	222	1	6
β-strand	224	1	6
β-strand	226-230	5	2
α-helix	231-233	3
α-helix	235-241	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Urokinase-type plasminogen activator	A	protein	245	Homo sapiens	P00749 (AlphaFold model)
bicyclic peptide UK18-D-Ser, uPA inhibitor	B	protein	18	Synthetic construct

Sequence of entity 1 (A), FASTA

>4JK5_1 Urokinase-type plasminogen activator (chains A)
IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVY
LGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTI
ALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTK
MLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPW
IRSHT

Sequence of entity 2 (B), FASTA

>4JK5_2 bicyclic peptide UK18-D-Ser, uPA inhibitor (chains B)
ACSRYEVDCRGRSSACGX

Ligands and cofactors

ID	Name	Formula	Copies
ZBR	1,3,5-tris(bromomethyl)benzene	C9 H9 Br3	1

Water and common crystallization additives (P6G, CL, SO4) are not listed.

Primary citation

Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids. Chen, S., Gfeller, D., Buth, S.A. et al. Chembiochem (2013) 14:1316-1322. DOI 10.1002/cbic.201300228 · PubMed

Other PDB entries of the same protein (UniProt P00749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YC6 1.18 Å, The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6
4ZKO 1.29 Å, The crystal structure of upain-1-W3A in complex with uPA at pH7.4
4ZKN 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH5.5
4ZKR 1.36 Å, The crystal structure of upain-1-W3A in complex with uPA at pH9.0
6XVD 1.4 Å, Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition
2O8T 1.45 Å, Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator…
3MHW 1.45 Å, The complex crystal Structure of Urokianse and 2-Aminobenzothiazole
5Z1C 1.45 Å, The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4
5WXF 1.46 Å, Crystal structure of uPA in complex with upain-2-2
4MNW 1.49 Å, Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic…
1GJ7 1.5 Å, Engineering inhibitors highly selective for the S1 sites of SER190 trypsin-like serine…
4XSK 1.5 Å, Structure of PAItrap, an uPA mutant

Browse structure collections

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