MolNFT v1 · #140288 · protein
Crystal structure of human SPINDLIN1 in complex with a histone H4K20(ME3) peptide
5Y5W · Spindlin-1: “Crystal structure of human SPINDLIN1 in complex with a histone H4K20(ME3) peptide”. X-ray diffraction, 7 pockets (best druggability 0.64). MolNFT v1 #140288 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y5W
- Type
- protein
- Length
- 822 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1; Histone peptide H4K20(ME3)
- UniProt
- Q9Y657
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 212 | 6% helix, 45% strand | Q9Y657 |
| B | Spindlin-1 | protein | 195 | 7% helix, 45% strand | Q9Y657 |
| C | Spindlin-1 | protein | 201 | 6% helix, 46% strand | Q9Y657 |
| D | Spindlin-1 | protein | 200 | 5% helix, 40% strand | Q9Y657 |
| E, G | Histone peptide H4K20(ME3) | protein | 5 | 0% helix, 40% strand | — |
| F | Histone peptide H4K20(ME3) | protein | 4 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.64 | 0.77 | 55 | empty |
| 2 | 516 | 0.60 | 0.74 | 57 | empty |
| 3 | 75 | 0.39 | 0.78 | 19 | empty |
| 4 | 55 | 0.36 | 0.79 | 16 | empty |
| 5 | 56 | 0.32 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1345 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 485 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 390 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 370 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 321 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 5Y5W · Crystal structure of human Spindlin1 in complex with a histone H4K20(me3) peptide · the same entry in another collection · chain G against G, TM-score 1.00
- Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · a predicted model of the same protein · chain D 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 Q9Y657
- Elsewhere: RCSB PDB 5Y5W · PDBe 5Y5W · UniProt Q9Y657
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