MolNFT v1 · #152262 · protein
Crystal structure of the spoc domain of human PHF3 in complex with RNA polymerase II ctd diheptapeptide phosphorylated on SER2
6IC8 · Phd finger protein 3: “Crystal structure of the spoc domain of human PHF3 in complex with RNA polymerase II ctd diheptapeptide…”. X-ray diffraction, 2 pockets (best druggability 0.33). MolNFT v1 #152262 on GenesisL1: 3D structure…
- PDB
- 6IC8
- Type
- protein
- Length
- 312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 3; Tyr-sep-pro-thr-ser-pro-ser-tyr-sep-pro-thr
- UniProt
- Q92576
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 3 | protein | 146 | 27% helix, 40% strand | Q92576 |
| B | Phd finger protein 3 | protein | 145 | 26% helix, 40% strand | Q92576 |
| C | Tyr-sep-pro-thr-ser-pro-ser-tyr-sep-pro-thr | protein | 11 | 0% helix, 18% strand | — |
| D | Tyr-sep-pro-thr-ser-pro-ser-tyr-sep-pro-thr | protein | 10 | 0% helix, 20% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.33 | 0.76 | 16 | empty |
| 2 | 72 | 0.30 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 652 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 573 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6IC8 · Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92576 · AlphaFold monomer V2.0 prediction for phd finger protein 3 (Q92576) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6IC8 · PDBe 6IC8 · UniProt Q92576
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