SMTL ID : 4rcp.1

Crystal structure of Plk1 Polo-box domain in complex with PL-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ACE- 56A- SER- TPO- NH2: PL-2(Non-covalent)

ACE-56A-SER-TPO-NH2.1: 17 residues within 4Å: Chain A: K.42, W.43, V.44, D.45, Y.46, Y.50, L.107, Y.110, F.111, Y.114, L.119, L.120, H.167, K.169 Ligands: EDO.2, EDO.4, EDO.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.44, A:Y.50, A:Y.50, A:L.107, A:Y.110, A:Y.110, A:Y.114, A:L.119 Hydrogen bonds: A:W.43, A:W.43, A:D.45, A:L.120 Water bridges: A:S.41, A:S.41, A:R.145, A:R.145, A:N.162, A:K.169, A:K.169 Salt bridges: A:H.167, A:K.169 pi-Stacking: A:Y.46, A:F.111

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: D.45, Y.46, S.47, D.48 Ligands: ACE-56A-SER-TPO-NH2.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.45, A:D.48, A:D.48 EDO.3: 3 residues within 4Å: Chain A: E.84, R.85, D.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.86, A:D.86 Water bridges: A:R.85 EDO.4: 2 residues within 4Å: Chain A: Y.50 Ligands: ACE-56A-SER-TPO-NH2.1 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: Y.110, N.113, Y.114 Ligands: ACE-56A-SER-TPO-NH2.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.110, A:Y.114 EDO.6: 6 residues within 4Å: Chain A: E.30, P.32, I.35, F.188, R.189, T.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.190, A:T.190 EDO.7: 3 residues within 4Å: Chain A: Y.82, S.100, L.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.82, A:Y.82, A:S.100 EDO.8: 5 residues within 4Å: Chain A: K.49, Y.50, F.65, N.66, D.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.66, A:D.67, A:D.67 EDO.9: 2 residues within 4Å: Chain A: W.143, F.144 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.143, A:W.143, A:W.143 EDO.10: 4 residues within 4Å: Chain A: F.163, Q.165, D.166, R.208 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: K.42, S.116, E.117, H.118, L.119, K.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.42, A:E.117 Water bridges: A:L.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, M. et al., A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1. J.Med.Chem. (2015)

Release Date

2014-11-12

Peptides

Serine/threonine-protein kinase PLK1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein kinase PLK1