SMTL ID : 5swk.1

Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: K.48, D.49, T.50 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: Q.74, H.76, K.97 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: K.48, D.49, T.50 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: M.65 Chain B: M.65 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: E.98, K.101 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: Q.74, H.76, K.97 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain D: T.13, T.14 Ligand excluded by PLIP

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

SO4.3: 4 residues within 4Å: Chain B: E.98, H.99, R.100, K.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.100, B:K.101 Salt bridges: B:R.100 SO4.8: 5 residues within 4Å: Chain C: S.42, E.43, G.44 Chain D: E.43, G.44 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.44, C:G.44 Water bridges: D:L.45, D:Q.75

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain C: Q.75, T.76 Chain D: K.19, Q.75, T.76 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.19, D:T.76, D:T.76, C:T.76, C:T.76, C:T.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jimenez-Sandoval, P. et al., Mimicking a p53-MDM2 interaction based on a stable immunoglobulin-like domain scaffold. Proteins (2018)

Release Date

2017-10-18

Peptides

E3 ubiquitin-protein ligase Mdm2: AB
De novo protein based on the inhibitor Amoebiasin-1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E3 ubiquitin-protein ligase Mdm2

De novo protein based on the inhibitor Amoebiasin-1