Research workbench
Crystal structure of the spoc domain of human PHF3 in complex with RNA polymerase II ctd diheptapeptide phosphorylated on SER2SER5
Analyse Crystal structure of the spoc domain of human PHF3 in complex with RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q5Y
- Type
- protein
- Length
- 614 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 3; PSER2PSER5
- UniProt
- Q92576
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phd finger protein 3 | protein | 149 | 19% helix, 30% strand | Q92576 |
| B | Phd finger protein 3 | protein | 148 | 21% helix, 32% strand | Q92576 |
| C | Phd finger protein 3 | protein | 148 | 21% helix, 37% strand | Q92576 |
| E, F | PSER2PSER5 | protein | 10 | 0% helix, 10% strand | — |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.79 | 0.86 | 80 | empty |
| 2 | 345 | 0.75 | 0.86 | 53 | empty |
| 3 | 76 | 0.60 | 0.88 | 19 | empty |
| 4 | 87 | 0.57 | 0.86 | 23 | empty |
| 5 | 65 | 0.57 | 0.89 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–F · 611 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 589 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 563 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 548 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 407 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 6Q5Y · Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD… · the same entry in another collection · chain F against F, TM-score 1.00
- Q92576 · AlphaFold monomer V2.0 prediction for phd finger protein 3 (Q92576) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q92576
- Elsewhere: RCSB PDB 6Q5Y · PDBe 6Q5Y · UniProt Q92576
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