MolNFT v1 · #168272 · protein
Crystal structure of PHF1 in complex with H3K36ME3 substitution
6WAV · Phd finger protein 1: “Crystal structure of PHF1 in complex with H3K36ME3 substitution”. X-ray diffraction, 2 ligands (UNX, SO4), 4 pockets (best druggability 0.47). MolNFT v1 #168272 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WAV
- Type
- protein
- Length
- 276 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 1; Histone H3.1
- UniProt
- O43189, P68431
- Ligands
- UNX, SO4
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 1 | protein | 59 | 5% helix, 51% strand | O43189 |
| B | Phd finger protein 1 | protein | 58 | 5% helix, 53% strand | O43189 |
| C, D | Phd finger protein 1 | protein | 60 | 5% helix, 50% strand | O43189 |
| E, F | Histone H3.1 | protein | 12 | 0% helix, 0% strand | P68431 |
| G | Histone H3.1 | protein | 8 | 0% helix, 0% strand | P68431 |
| H | Histone H3.1 | protein | 7 | 0% helix, 0% strand | P68431 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 44 copies · chains A, C, E, B, D, F, G, H
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.47 | 0.76 | 24 | UNX |
| 2 | 165 | 0.46 | 0.76 | 24 | UNX |
| 3 | 56 | 0.32 | 0.76 | 14 | UNX |
| 4 | 55 | 0.28 | 0.74 | 16 | UNX |
Interfaces
13 interfaces between chains.
- B–F · 546 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 531 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 399 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 6WAV · Crystal structure of PHF1 in complex with H3K36me3 substitution · the same entry in another collection · chain H against H, TM-score 1.00
- O43189 · AlphaFold monomer V2.0 prediction for phd finger protein 1 (O43189) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain H against A, TM-score 0.67
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 O43189
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 6WAV · PDBe 6WAV · UniProt O43189 · UniProt P68431
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