SMTL ID : 4gly.1

Human urokinase-type plasminogen activator uPA in complex with the two-disulfide bridge peptide UK504

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: A.89, D.90, T.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.89, A:D.90, A:T.91, A:T.91 SO4.2: 3 residues within 4Å: Chain A: Q.169, P.170, H.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.171 Salt bridges: A:H.171 SO4.8: 3 residues within 4Å: Chain A: R.20, H.22, R.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.23 Water bridges: A:R.20 Salt bridges: A:R.20, A:H.22 SO4.9: 4 residues within 4Å: Chain A: I.162, S.163, H.164 Ligands: CL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.164, A:R.233 Water bridges: A:F.131, A:H.164, A:H.164 Salt bridges: A:H.164

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: S.37, P.38, C.39, W.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.37, A:C.39 NA.5: 4 residues within 4Å: Chain A: I.9, E.10, S.64, T.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.64, A:S.64 Water bridges: A:Q.71

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

CL.4: 3 residues within 4Å: Chain A: R.220, G.221 Chain B: G.4 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: I.162, H.164, L.182, C.183 Ligands: SO4.9 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: N.96 Ligand excluded by PLIP

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

P6G.10: 7 residues within 4Å: Chain A: V.27, T.28, Y.29, N.67, Y.148, L.149, Y.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28, A:T.28 Water bridges: A:Y.150

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: E.166, Q.169, H.171, Y.172, K.225, D.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.169, A:Y.172, A:D.226 Water bridges: A:K.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Bicyclic Peptide Ligands Pulled out of Cysteine-Rich Peptide Libraries. J.Am.Chem.Soc. (2013)

Release Date

2013-05-15

Peptides

Urokinase-type plasminogen activator: A
BICYCLIC PEPTIDE INHIBITOR UK504: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Urokinase-type plasminogen activator

BICYCLIC PEPTIDE INHIBITOR UK504

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