SMTL ID : 8f13.1

Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon Polypeptide, alternative C-terminus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: R.13, P.14, K.15, P.16 No protein-ligand interaction detected (PLIP) EDO.2: 6 residues within 4Å: Chain A: C.61, S.62, G.67, D.68, V.72, P.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.61 EDO.3: 1 residues within 4Å: Chain A: S.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74 EDO.4: 4 residues within 4Å: Chain A: K.54, Q.55, Q.56, H.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.56 Water bridges: A:Q.56, A:H.57 EDO.8: 3 residues within 4Å: Chain B: P.3, E.7, C.8 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: S.6 Chain B: C.15, Q.16, Q.17, V.18 No protein-ligand interaction detected (PLIP)

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

SO4.5: 4 residues within 4Å: Chain A: E.79, H.80, R.81 Chain B: Q.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.80, A:R.81 Water bridges: A:K.82 Salt bridges: A:R.81

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

DMS.6: 4 residues within 4Å: Chain A: F.70, G.71, V.72, R.89 No protein-ligand interaction detected (PLIP)

1 x WHL: N,N'-(1,4-phenylene)diacetamide(Non-covalent)

WHL.7: 6 residues within 4Å: Chain A: K.35 Chain B: C.8, A.11, A.12, C.15, Q.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Callahan, A.J. et al., Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display. Chemrxiv (2023)

Release Date

2023-02-15

Peptides

E3 ubiquitin-protein ligase Mdm2: A
H103: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase Mdm2

H103

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