Research workbench
Crystal structure of maize SHH2 sawadee domain in complex with an H3K9ME3 peptide
Analyse Crystal structure of maize SHH2 sawadee domain in complex with an H3K9ME3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EF2
- Type
- protein
- Length
- 305 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hb transcription factor; Histone H3.2
- UniProt
- B7ZYP9, P69246
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hb transcription factor | protein | 148 | 19% helix, 44% strand | B7ZYP9 |
| B | Hb transcription factor | protein | 142 | 18% helix, 46% strand | B7ZYP9 |
| P | Histone H3.2 | protein | 8 | 0% helix, 13% strand | P69246 |
| Q | Histone H3.2 | protein | 7 | 0% helix, 14% strand | P69246 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.75 | 0.77 | 86 | empty |
| 2 | 63 | 0.42 | 0.81 | 13 | empty |
| 3 | 51 | 0.38 | 0.81 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–P · 774 Ų buried · 13 hydrogen bonds · protein-protein
- B–Q · 627 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 525 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 7EF2 · Crystal structure of maize SHH2 SAWADEE domain in complex with an H3K9me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P69246 · AlphaFold monomer V2.0 prediction for histone H3.2 (P69246) · a predicted model of the same protein · chain P against A, TM-score 0.55
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 B7ZYP9
- Every structure of UniProt P69246
- Elsewhere: RCSB PDB 7EF2 · PDBe 7EF2 · UniProt B7ZYP9 · UniProt P69246
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.