Research workbench
Crystal structure of SGF29 in complex with H3K4ME2
Analyse Crystal structure of SGF29 in complex with H3K4ME2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MET
- Type
- protein
- Length
- 360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saga-associated factor 29 homolog; Histone H3
- UniProt
- Q96ES7, Q92133
- Ligands
- UNX, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saga-associated factor 29 homolog | protein | 174 | 14% helix, 37% strand | Q96ES7 |
| B | Saga-associated factor 29 homolog | protein | 174 | 11% helix, 37% strand | Q96ES7 |
| C | Histone H3 | protein | 8 | 50% helix, 0% strand | Q92133 |
| D | Histone H3 | protein | 4 | 0% helix, 0% strand | Q92133 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.82 | 0.83 | 78 | empty |
| 2 | 106 | 0.45 | 0.79 | 15 | GOL |
| 3 | 99 | 0.45 | 0.79 | 21 | empty |
| 4 | 75 | 0.36 | 0.77 | 18 | empty |
| 5 | 79 | 0.33 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 685 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 325 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered, 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 Q96ES7
- Every structure of UniProt Q92133
- Elsewhere: RCSB PDB 3MET · PDBe 3MET · UniProt Q96ES7 · UniProt Q92133
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