5YC6: UPA

The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6. Determined by X-ray diffraction at 1.18 Å resolution. Released 3 Oct 2018.

Method: X-ray diffraction
Resolution: 1.18 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,190
Mol. weight: 28.3 kDa
Ligands: PZH
Released: 3 Oct 2018

Explore 5YC6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YC6 contains 12 α-helices and 24 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 U: 12 helices, 24 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
α-helix	37	1
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
α-helix	76-77	2
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	115	1	6
β-strand	118	1	6
β-strand	122	1	2
α-helix	123-125	3
α-helix	130-131	2
β-strand	135-140	6	2
α-helix	151-152	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	7
β-strand	224	1	7
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	U	protein	246	Homo sapiens	P00749 (AlphaFold model)

Sequence of entity 1 (U), FASTA

>5YC6_1 Urokinase-type plasminogen activator (chains U)
IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVY
LGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTI
ALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTK
MLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPW
IRSHTK

Ligands and cofactors

ID	Name	Formula	Copies
PZH	1-(4-bromophenyl)methanamine	C7 H8 Br N	1

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

Primary citation

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases. Jiang, L.G., Zhang, X., Zhou, Y. et al. RSC Adv (2018) 8:28189-28197. DOI 10.1039/c8ra03145b

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

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
4GLY 1.52 Å, Human urokinase-type plasminogen activator uPA in complex with the two-disulfide bridge…

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