SMTL ID : 4mnv.1

Crystal structure of bicyclic peptide UK729 bound as an acyl-enzyme intermediate to urokinase-type plasminogen activator (uPA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x THR- CYS- PRO- NH2: acyl-enzyme intermediate of bicyclic peptide UK729(Non-covalent)

THR-CYS-PRO-NH2.1: 4 residues within 4Å: Chain A: R.220 Chain B: Q.4 Ligands: ZBR.5, GOL.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.220 Hydrogen bonds: B:Q.4

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

SO4.2: 4 residues within 4Å: Chain A: H.95, N.96, T.178, K.180 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.96, A:T.178 Water bridges: A:H.95 Salt bridges: A:H.95, A:K.180

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

ACT.3: 1 residues within 4Å: Chain A: R.109 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.109 ACT.4: 2 residues within 4Å: Chain A: S.243, T.245 No protein-ligand interaction detected (PLIP)

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

ZBR.5: 5 residues within 4Å: Chain B: C.2, R.3, Q.4, C.7 Ligands: THR-CYS-PRO-NH2.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.4

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Ligands: THR-CYS-PRO-NH2.1 No protein-ligand interaction detected (PLIP)

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
acyl-enzyme intermediate of bicyclic peptide UK729: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator chain B

acyl-enzyme intermediate of bicyclic peptide UK729

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