Research workbench
Crystal structure of SPINDLIN1 bound to H3(K4ME3-K9ME3) peptide
Analyse Crystal structure of SPINDLIN1 bound to H3(K4ME3-K9ME3) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BQZ
- Type
- protein
- Length
- 875 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1; H3(K4ME3-K9ME3) peptide
- UniProt
- Q9Y657, Q71DI3
- Pockets
- 13 · best druggability 0.53
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 215 | 2% helix, 39% strand | Q9Y657 |
| B | H3(K4ME3-K9ME3) peptide | protein | 13 | 31% helix, 8% strand | Q71DI3 |
| C | Spindlin-1 | protein | 208 | 3% helix, 41% strand | Q9Y657 |
| D, F, H | H3(K4ME3-K9ME3) peptide | protein | 10 | 30% helix, 20% strand | Q71DI3 |
| E | Spindlin-1 | protein | 204 | 6% helix, 42% strand | Q9Y657 |
| G | Spindlin-1 | protein | 205 | 7% helix, 42% strand | Q9Y657 |
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.53 | 0.79 | 24 | empty |
| 2 | 116 | 0.50 | 0.81 | 22 | empty |
| 3 | 162 | 0.41 | 0.73 | 27 | empty |
| 4 | 132 | 0.40 | 0.74 | 21 | empty |
| 5 | 120 | 0.37 | 0.74 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1263 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 1226 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 957 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 872 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation).
Compared structures
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
- Every structure of UniProt Q71DI3
- Elsewhere: RCSB PDB 7BQZ · PDBe 7BQZ · UniProt Q9Y657 · UniProt Q71DI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.