MolNFT v1 · #177329 · protein
Crystal structure of maize SHH2 sawadee domain in complex with and H3K9ME1 peptide
7EF1 · Hb transcription factor: “Crystal structure of maize SHH2 sawadee domain in complex with and H3K9ME1 peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.75). MolNFT v1 #177329 on GenesisL1: 3D structure…
- PDB
- 7EF1
- Type
- protein
- Length
- 306 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
- 2 · 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, 45% strand | B7ZYP9 |
| P | Histone H3.2 | protein | 9 | 0% helix, 11% 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.75 | 0.78 | 72 | empty |
| 2 | 54 | 0.37 | 0.80 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–P · 823 Ų buried · 21 hydrogen bonds · protein-protein
- B–Q · 608 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 538 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 7EF1 · crystal structure of maize SHH2 SAWADEE domain in complex with and H3K9me1 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 Q against A, TM-score 0.56
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 7EF1 · PDBe 7EF1 · UniProt B7ZYP9 · UniProt P69246
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