Research workbench
Structure of human MDM2 in complex with high affinity peptide
Analyse Structure of human MDM2 in complex with high affinity peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G03
- Type
- protein
- Length
- 192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; High affinity synthetic peptide
- EC
- 6.3.2.-
- UniProt
- Q00987
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 87 | 45% helix, 18% strand | Q00987 |
| B, D | High affinity synthetic peptide | protein | 11 | 55% helix, 0% strand | — |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 47% helix, 16% strand | Q00987 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.72 | 0.85 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 583 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 530 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3G03 · Structure of human MDM2 in complex with high affinity peptide · the same entry in another collection · chain A against A, 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 Q00987
- Elsewhere: RCSB PDB 3G03 · PDBe 3G03 · UniProt Q00987
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