MolNFT v1 · #100501 · protein
Crystal structure of human SPINDLIN1 bound to histone H3K4ME3 peptide
4MZG · Peptide from histone H3.2: “Crystal structure of human SPINDLIN1 bound to histone H3K4ME3 peptide”. X-ray diffraction, 2 ligands (MG, CL), 9 pockets (best druggability 0.58). MolNFT v1 #100501 on GenesisL1: 3D structure, binding…
- PDB
- 4MZG
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide from histone H3.2; Spindlin-1
- UniProt
- Q71DI3, Q9Y657
- Ligands
- MG, CL
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide from histone H3.2 | protein | 9 | 0% helix, 22% strand | Q71DI3 |
| B | Spindlin-1 | protein | 196 | 7% helix, 48% strand | Q9Y657 |
| C | Peptide from histone H3.2 | protein | 6 | 0% helix, 33% strand | Q71DI3 |
| D | Spindlin-1 | protein | 191 | 7% helix, 48% strand | Q9Y657 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, D
- CL · Chloride ion · ion · 3 copies · chains B, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.58 | 0.86 | 15 | MRD |
| 2 | 146 | 0.54 | 0.81 | 20 | MG, CL |
| 3 | 55 | 0.48 | 0.84 | 9 | MPD |
| 4 | 82 | 0.44 | 0.80 | 17 | empty |
| 5 | 126 | 0.41 | 0.75 | 19 | MPD |
Interfaces
3 interfaces between chains.
- A–B · 686 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 556 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 369 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4MZG · Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide · the same entry in another collection · chain D against D, 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 0.98
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain C against A, TM-score 0.73
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 Q71DI3
- Every structure of UniProt Q9Y657
- Elsewhere: RCSB PDB 4MZG · PDBe 4MZG · UniProt Q71DI3 · UniProt Q9Y657
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.