Research workbench
Ternary complex of PHF1, a DNA duplex and a histone peptide
Analyse Ternary complex of PHF1, a DNA duplex and a histone peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XFQ
- Type
- protein + DNA
- Length
- 651 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 1; DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3'); Peptide from…
- UniProt
- Q9Z1B8, Q5TEC6
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 1 | protein | 312 | 26% helix, 20% strand | Q9Z1B8 |
| B | Phd finger protein 1 | protein | 300 | 24% helix, 20% strand | Q9Z1B8 |
| C | DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') | dna | 13 | — | — |
| D | DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') | dna | 12 | — | — |
| E, F | Peptide from histone H3 | protein | 7 | 0% helix, 0% strand | Q5TEC6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.84 | 0.85 | 123 | empty |
| 2 | 122 | 0.40 | 0.75 | 24 | empty |
| 3 | 115 | 0.39 | 0.75 | 17 | empty |
| 4 | 115 | 0.39 | 0.75 | 22 | empty |
| 5 | 82 | 0.38 | 0.77 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 760 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 638 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 627 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- A–C · 311 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5XFQ · Ternary complex of PHF1, a DNA duplex and a histone peptide · the same entry in another collection · chain F against F, TM-score 1.00
- Q9Z1B8 · AlphaFold monomer V2.0 prediction for phd finger protein 1 (Q9Z1B8) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain E against A, TM-score 0.53
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 Q9Z1B8
- Every structure of UniProt Q5TEC6
- Elsewhere: RCSB PDB 5XFQ · PDBe 5XFQ · UniProt Q9Z1B8 · UniProt Q5TEC6
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