MolNFT v1 · #118735 · protein
Crystal structure of a phd finger bound to histone H3 T3PH peptide
5FB0 · Nuclear autoantigen sp-100: “Crystal structure of a phd finger bound to histone H3 T3PH peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.59). MolNFT v1 #118735 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FB0
- Type
- protein
- Length
- 362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear autoantigen sp-100; Peptide from histone H3
- UniProt
- P23497, K7EMV3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear autoantigen sp-100 | protein | 172 | 48% helix, 7% strand | P23497 |
| D, F | Peptide from histone H3 | protein | 10 | 0% helix, 50% strand | K7EMV3 |
| C | Nuclear autoantigen sp-100 | protein | 170 | 51% helix, 7% strand | P23497 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.59 | 0.75 | 54 | empty |
| 2 | 108 | 0.50 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 657 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 642 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 409 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5FB0 · Crystal Structure of a PHD finger bound to histone H3 T3ph peptide · the same entry in another collection · chain A against A, TM-score 1.00
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 P23497
- Every structure of UniProt K7EMV3
- Elsewhere: RCSB PDB 5FB0 · PDBe 5FB0 · UniProt P23497 · UniProt K7EMV3
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