SMTL ID : 4mny.1 (1 other biounit)

Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-oligomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: H.22, R.23 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.23 Water bridges: A:R.20, A:R.20, A:R.20 Salt bridges: A:H.22, A:R.23 SO4.2: 4 residues within 4Å: Chain A: V.27, T.28, Y.29, Y.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.27, A:Y.29 Water bridges: A:N.67, A:Y.150

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

ACT.3: 7 residues within 4Å: Chain A: V.30, H.46, Q.195, G.196, D.197, S.198 Chain B: Y.6 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.196, A:S.198, A:S.198, B:Y.6 Water bridges: A:H.46, A:Q.195, B:V.4, B:V.4 Salt bridges: A:H.46 ACT.4: 2 residues within 4Å: Chain A: R.242, T.245 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: H.95, N.96, T.178, K.180, M.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.96, A:N.96 GOL.6: 4 residues within 4Å: Chain A: F.131, S.163, H.164, R.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.164, A:R.165

1 x 29O: N,N',N''-benzene-1,3,5-triyltris(2-bromoacetamide)(Covalent)

29O.7: 17 residues within 4Å: Chain A: K.142, S.145, T.146, D.147, Y.148, C.194, Q.195, G.221, C.222 Chain B: G.1, C.2, N.5, C.7, P.8, P.9, V.10, C.12 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.5, B:C.7, A:S.145 Hydrophobic interactions: A:Q.195 Water bridges: A:K.142

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 UK903: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Urokinase-type plasminogen activator chain B

bicyclic peptide UK903

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