Research workbench
Crystal structure of human MDM2 ring domain homodimer bound to UBCH5B- ub
Analyse Crystal structure of human MDM2 ring domain homodimer bound to UBCH5B- ub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SQO
- Type
- protein
- Length
- 570 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Ubiquitin-conjugating enzyme E2 D2; Ubiquitin-40S…
- EC
- 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- Q00987, P62837, J3QTR3
- Ligands
- ZN, CL, NO3
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 62 | 21% helix, 27% strand | Q00987 |
| B, E | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 21% strand | P62837 |
| C, F | Ubiquitin-40S ribosomal protein S27A | protein | 77 | 19% helix, 36% strand | J3QTR3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E
- NO3 · Nitrate ion · ion · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.63 | 0.83 | 38 | empty |
| 2 | 155 | 0.62 | 0.85 | 26 | empty |
| 3 | 62 | 0.42 | 0.81 | 17 | empty |
| 4 | 89 | 0.37 | 0.76 | 16 | empty |
| 5 | 89 | 0.35 | 0.74 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1228 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 955 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 943 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 516 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 6SQO · Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub · the same entry in another collection · chain B against B, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain B against A, TM-score 0.98
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
- Every structure of UniProt P62837
- Every structure of UniProt J3QTR3
- Elsewhere: RCSB PDB 6SQO · PDBe 6SQO · UniProt Q00987 · UniProt P62837 · UniProt J3QTR3
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