MolNFT v1 · #161172 · protein
Crystal structure of the spoc domain of human PHF3 in complex with RNA polymerase II ctd diheptapeptide phosphorylated on SER2SER5
6Q5Y · Phd finger protein 3: “Crystal structure of the spoc domain of human PHF3 in complex with RNA polymerase II ctd diheptapeptide…”. X-ray diffraction, 14 pockets (best druggability 0.79). MolNFT v1 #161172 on GenesisL1: 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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