SMTL ID : 4mnw.1

Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK749

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-oligomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.95, T.178, K.180, M.181 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.178 Salt bridges: A:H.95, A:K.180 SO4.2: 3 residues within 4Å: Chain A: S.163, H.164, R.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.164, A:R.165

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.8, S.64, R.65, T.70, Q.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.64, A:Q.153 Water bridges: A:Q.71 GOL.4: 4 residues within 4Å: Chain A: H.164, Q.168, T.178, T.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.164, A:Q.168, A:T.179 Water bridges: A:T.179 GOL.5: 4 residues within 4Å: Chain A: R.20, H.22, R.23, Y.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.20, A:R.20, A:H.22, A:R.23, A:Y.51 GOL.6: 11 residues within 4Å: Chain A: H.94, H.95, N.96, D.97, K.180, M.181, S.217, W.218, T.232, F.237 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.96, A:D.97, A:S.217, A:W.218 GOL.7: 4 residues within 4Å: Chain A: I.2, W.189, K.190, A.223 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: S.124, M.125, R.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.125 Salt bridges: A:R.242

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

ZBR.9: 5 residues within 4Å: Chain A: Q.195 Chain B: C.2, C.7, R.10, C.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Peptide ligands stabilized by small molecules. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-02-05

Peptides

Urokinase-type plasminogen activator chain B: A
bicyclic peptide UK749: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator chain B

bicyclic peptide UK749

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