MolNFT v1 · #147098 · protein
Ubiquitin in complex with PT(2-PHENILPYRIDINE)(PPH3)
6E2B: “Ubiquitin in complex with PT(2-PHENILPYRIDINE)(PPH3)”. X-ray diffraction, 2 ligands (PT7, SO4), 4 pockets (best druggability 0.86). MolNFT v1 #147098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E2B
- Type
- protein
- Length
- 456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P62992
- Ligands
- PT7, SO4
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, P | Ubiquitin | protein | 76 | 24% helix, 32% strand | P62992 |
Ligands and binding sites
- PT7 · chloro[2-(pyridin-2-yl-kappaN)phenyl-kappaC~1~](triphenyl-lambda~5~-phosphanyl)platinum(2+) · ligand · 3 copies · chains A, G, I, P, C, E
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, G, E, I, P
- GOL · Glycerol · additive · 8 copies · chains A, C, E, P, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.86 | 0.86 | 109 | PT7, GOL, SO4 |
| 2 | 58 | 0.68 | 0.95 | 14 | empty |
| 3 | 51 | 0.68 | 0.96 | 14 | empty |
| 4 | 100 | 0.35 | 0.73 | 20 | empty |
Interfaces
12 interfaces between chains.
- A–G · 897 Ų buried · 16 hydrogen bonds · protein-protein
- I–P · 811 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 775 Ų buried · 13 hydrogen bonds · protein-protein
- E–I · 371 Ų buried · 1 hydrogen bond · protein-protein
- G–I · 367 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6E2B · Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3) · the same entry in another collection · chain E against E, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P62992
- Elsewhere: RCSB PDB 6E2B · PDBe 6E2B · UniProt P62992
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