SMTL ID : 4jk5.1

Human urokinase-type Plasminogen Activator (uPA) in complex with a bicyclic peptide inhibitor (UK18-D-Ser)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.54, E.79, N.80, L.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79, A:L.81 Salt bridges: A:K.54 SO4.2: 1 residues within 4Å: Chain A: T.8 No protein-ligand interaction detected (PLIP) SO4.3: 2 residues within 4Å: Chain A: S.68, N.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.69, A:N.69 SO4.4: 5 residues within 4Å: Chain A: R.20, H.22, R.23, Y.51 Chain B: R.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.23 Salt bridges: A:R.20, A:H.22

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: L.83, H.84, K.85, W.240, H.244 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: H.22, G.24, G.25, S.26 Chain B: Y.5 Ligand excluded by PLIP

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.7: 2 residues within 4Å: Chain A: N.67, L.149 No protein-ligand interaction detected (PLIP)

1 x ZBR: 1,3,5-tris(bromomethyl)benzene(Covalent)

ZBR.8: 4 residues within 4Å: Chain A: D.50 Chain B: C.2, C.9, C.16 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids. Chembiochem (2013)

Release Date

2013-07-17

Peptides

Urokinase-type plasminogen activator: A
bicyclic peptide UK18-D-Ser, uPA inhibitor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator

bicyclic peptide UK18-D-Ser, uPA inhibitor

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