MolNFT v1 · #153083 · protein
Crystal structure of saccharomyces cerevisiae SPP1 in complex with H3K4ME3
6J2P · Compass component SPP1: “Crystal structure of saccharomyces cerevisiae SPP1 in complex with H3K4ME3”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.45). MolNFT v1 #153083 on GenesisL1: 3D structure, binding sites…
- PDB
- 6J2P
- Type
- protein
- Length
- 398 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Compass component SPP1; Histone H3
- UniProt
- Q03012, P61830
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Compass component SPP1 | protein | 98 | 14% helix, 15% strand | Q03012 |
| B | Compass component SPP1 | protein | 93 | 11% helix, 16% strand | Q03012 |
| C | Compass component SPP1 | protein | 90 | 12% helix, 17% strand | Q03012 |
| D | Compass component SPP1 | protein | 92 | 8% helix, 16% strand | Q03012 |
| E | Histone H3 | protein | 7 | 0% helix, 29% strand | P61830 |
| F, G, H | Histone H3 | protein | 6 | 0% helix, 33% strand | P61830 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.45 | 0.77 | 22 | empty |
| 2 | 134 | 0.44 | 0.76 | 20 | empty |
| 3 | 127 | 0.42 | 0.76 | 21 | empty |
| 4 | 108 | 0.41 | 0.76 | 17 | empty |
| 5 | 65 | 0.34 | 0.77 | 16 | empty |
Interfaces
12 interfaces between chains.
- A–E · 577 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 567 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 543 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 501 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 453 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 6J2P · Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 · the same entry in another collection · chain H against H, TM-score 1.00
- Q03012 · AlphaFold monomer V2.0 prediction for compass component SPP1 (Q03012) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q03012
- Every structure of UniProt P61830
- Elsewhere: RCSB PDB 6J2P · PDBe 6J2P · UniProt Q03012 · UniProt P61830
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