PDBsum entry 4gly

Hydrolase/hydrolase inhibitor

PDB id: 4gly

Contents

Protein chains

245 a.a.

14 a.a.

Ligands

SO4 ×4

P6G

GOL

Metals

_NA ×2

_CL ×3

Waters ×310

PDB id:

4gly

Name:

Hydrolase/hydrolase inhibitor

Title:

Human urokinase-type plasminogen activator upa in complex with the two-disulfide bridge peptide uk504

Structure:

Urokinase-type plasminogen activator. Chain: a. Fragment: catalytic domain, urokinase-type plasminogen activator. Synonym: u-plasminogen activator, upa, urokinase-type plasminogen activator long chain a, urokinase-type plasminogen activator short chain a, urokinase-type plasminogen activator chain b. Engineered: yes. Mutation: yes. Bicyclic peptide inhibitor uk504.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: 9606. Gene: plau. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek-293. Synthetic: yes.

Resolution:

1.52Å R-factor: 0.132 R-free: 0.204

Authors:

S.A.Buth,P.G.Leiman,S.Chen,C.Heinis

Key ref:

S.Chen et al. (2013). Bicyclic peptide ligands pulled out of cysteine-rich peptide libraries. J Am Chem Soc, 135, 6562-6569. PubMed id: 23560397 DOI: 10.1021/ja400461h

Date:

15-Aug-12 Release date: 15-May-13

Protein chain

P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator from Homo sapiens

Seq: 431 a.a.

Struc: 245 a.a.*

Protein chain

No UniProt id for this chain

Struc: 14 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.73 - u-plasminogen activator.
• Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

DOI no: 10.1021/ja400461h

J Am Chem Soc 135:6562-6569 (2013)

PubMed id: 23560397

Bicyclic peptide ligands pulled out of cysteine-rich peptide libraries.

S.Chen, I.Rentero Rebollo, S.A.Buth, J.Morales-Sanfrutos, J.Touati, P.G.Leiman, C.Heinis.

ABSTRACT

Bicyclic peptide ligands were found to have good binding affinity and target specificity. However, the method applied to generate bicyclic ligands based on phage-peptide alkylation is technically complex and limits its application to specialized laboratories. Herein, we report a method that involves a simpler and more robust procedure that additionally allows screening of structurally more diverse bicyclic peptide libraries. In brief, phage-encoded combinatorial peptide libraries of the format XmCXnCXoCXp are oxidized to connect two pairs of cysteines (C). This allows the generation of 3 × (m + n + o + p) different peptide topologies because the fourth cysteine can appear in any of the (m + n + o + p) randomized amino acid positions (X). Panning of such libraries enriched strongly peptides with four cysteines and yielded tight binders to protein targets. X-ray structure analysis revealed an important structural role of the disulfide bridges. In summary, the presented approach offers facile access to bicyclic peptide ligands with good binding affinities.