SMTL ID : 7qdq.1

Crystal Structure of HDM2 in complex with Caylin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: E.6, T.7, T.30, M.31, K.32 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.12, P.13, L.14 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: E.76, K.79 Ligands: DMS.8 Ligand excluded by PLIP

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

NA.4: 3 residues within 4Å: Chain A: D.49, Q.52, I.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.49, A:Q.52 NA.5: 2 residues within 4Å: Chain A: V.89, V.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.90

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

SO4.6: 1 residues within 4Å: Chain A: K.51 No protein-ligand interaction detected (PLIP)

1 x AU0: Caylin-1(Non-covalent)

AU0.7: 17 residues within 4Å: Chain A: L.35, L.38, G.39, Q.40, I.42, M.43, Y.48, Q.53, H.54, V.56, F.67, F.72, V.74, H.77, I.80, Y.81, I.84 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.35, A:I.42, A:V.56, A:V.74, A:V.74 Hydrogen bonds: A:Q.40 pi-Stacking: A:H.77 Halogen bonds: A:H.77

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 7 residues within 4Å: Chain A: K.75, E.76, H.77, R.78, K.79, I.80 Ligands: CL.3 No protein-ligand interaction detected (PLIP) DMS.9: 4 residues within 4Å: Chain A: Q.25, K.26, D.27, T.28 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mertens, V. et al., Elucidation of a nutlin-derivative-HDM2 complex structure at the interaction site by NMR molecular replacement: A straightforward derivation. J Magn Reson Open (2022)

Release Date

2022-10-05

Peptides

E3 ubiquitin-protein ligase Mdm2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase Mdm2

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