MolNFT v1 · #137293 · protein
Crystal structure of human MDM4 in complex with a 12-mer lysine- cysteine side chain dithiocarbamate stapled peptide inhibitor pmi
5VK1 · Protein MDM4: “Crystal structure of human MDM4 in complex with a 12-mer lysine- cysteine side chain dithiocarbamate stapled…”. X-ray diffraction, 2 ligands (ACE, NH2), 9 pockets (best druggability 0.80). MolNFT v1 #137293 on…
- PDB
- 5VK1
- Type
- protein
- Length
- 747 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein MDM4; Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor pmi
- UniProt
- O15151
- Ligands
- ACE, NH2
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Protein MDM4 | protein | 83 | 49% helix, 13% strand | O15151 |
| B, D, J | Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor pmi | protein | 12 | 42% helix, 0% strand | — |
| C, G, M, O | Protein MDM4 | protein | 82 | 49% helix, 13% strand | O15151 |
| F, P | Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor pmi | protein | 10 | 50% helix, 0% strand | — |
| H, L, N | Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor pmi | protein | 11 | 73% helix, 0% strand | — |
| I, K | Protein MDM4 | protein | 82 | 48% helix, 15% strand | O15151 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains B, D, F, H, J, L, K, N, P
- NH2 · Amino group · ion · 3 copies · chains A, B, J, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.80 | 0.81 | 68 | ACE |
| 2 | 507 | 0.69 | 0.79 | 75 | empty |
| 3 | 254 | 0.54 | 0.76 | 32 | empty |
| 4 | 198 | 0.51 | 0.76 | 20 | empty |
| 5 | 292 | 0.51 | 0.73 | 31 | empty |
Interfaces
31 interfaces between chains.
- C–D · 553 Ų buried · 1 hydrogen bond · protein-protein
- I–J · 543 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 531 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 2 hydrogen bonds · protein-protein
- O–P · 521 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 5VK1 · Crystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain… · the same entry in another collection · chain P against P, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O15151
- Elsewhere: RCSB PDB 5VK1 · PDBe 5VK1 · UniProt O15151
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