MolNFT v1 · #69594 · protein
Structure of PHF8 in complex with histone H3
3KV4 · Phd finger protein 8: “Structure of PHF8 in complex with histone H3”. X-ray diffraction, 4 ligands (OGA, ZN, FE2), 7 pockets (best druggability 0.83). MolNFT v1 #69594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KV4
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 8; Histone H3-like
- EC
- 2.-.-.-
- UniProt
- Q9UPP1, Q6NXT2
- Ligands
- OGA, ZN, FE2, NI
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 8 (EC 2.-.-.-) | protein | 432 | 39% helix, 21% strand | Q9UPP1 |
| B | Histone H3-like | protein | 14 | 0% helix, 7% strand | Q6NXT2 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A
- FE2 · Fe (II) ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.83 | 0.97 | 25 | empty |
| 2 | 132 | 0.61 | 0.86 | 28 | empty |
| 3 | 123 | 0.45 | 0.77 | 20 | EDO |
| 4 | 118 | 0.38 | 0.74 | 25 | empty |
| 5 | 103 | 0.36 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1384 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3KV4 · Structure of PHF8 in complex with histone H3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UPP1 · AlphaFold monomer V2.0 prediction for histone lysine demethylase PHF8 (Q9UPP1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6NXT2 · AlphaFold monomer V2.0 prediction for histone H3.3C (Q6NXT2) · a predicted model of the same protein · chain B against A, TM-score 0.21
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 Q9UPP1
- Every structure of UniProt Q6NXT2
- Elsewhere: RCSB PDB 3KV4 · PDBe 3KV4 · UniProt Q9UPP1 · UniProt Q6NXT2
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