› 8f0z

X-ray diffraction
1.61Å resolution

Structure of the MDM2 P53 binding domain in complex with H101, an all-D Helicon Polypeptide

Released:
DOI: 10.2210/pdb8f0z/pdb
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PDB entry 8f0z coloured by chain, front view.
PDB entry 8f0z coloured by chain, side view.
PDB entry 8f0z coloured by chain, top view.
Source organisms:
Primary publication:
Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display
Callahan AJ, Gandhesiri S, Travaline TL, Lozano Salazar L, Hanna S, Lee Y-C, Li K, Tokareva OS, Swiecicki J-M, Loas A, Verdine GL, McGee JH, Pentelute BL
Chemrxiv (2023)

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-274345 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase Mdm2 Chain: A
Molecule details ›
Chain: A
Length: 95 amino acids
Theoretical weight: 11.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00987 (Residues: 17-111; Coverage: 19%)
Gene name: MDM2
Sequence domains: SWIB/MDM2 domain
H101 Chain: B
Molecule details ›
Chain: B
Length: 19 amino acids
Theoretical weight: 2 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand WHL 1 x WHL
12 modified residues:
Ligand DAS 2 x DAS
Ligand DPR 1 x DPR
Ligand DAL 3 x DAL
Ligand DHI 1 x DHI
Ligand DTR 1 x DTR
Ligand DTY 1 x DTY
Ligand DCY 2 x DCY
Ligand DPN 2 x DPN
Ligand DGN 1 x DGN
Ligand DVA 1 x DVA
Ligand DSG 1 x DSG
Ligand DSN 1 x DSN

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21212
Unit cell:
a: 40.871Å b: 81.357Å c: 34.975Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.221 0.242
Expression systems:
  • Escherichia coli
  • Not provided

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