Research workbench
Crystal structure of TAF3 phd finger bound to H3K4ME3Q5SER
Analyse Crystal structure of TAF3 phd finger bound to H3K4ME3Q5SER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XMY
- Type
- protein
- Length
- 138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor tfiid subunit 3; Histone peptide H3(1-15)K4ME3Q5SER
- UniProt
- Q5VWG9
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription initiation factor tfiid subunit 3 | protein | 63 | 11% helix, 22% strand | Q5VWG9 |
| P, D | Histone peptide H3(1-15)K4ME3Q5SER | protein | 7 | 0% helix, 43% strand | — |
| C | Transcription initiation factor tfiid subunit 3 | protein | 61 | 7% helix, 26% strand | Q5VWG9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.57 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–P · 562 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
- P–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5XMY · Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser · the same entry in another collection · chain A against A, TM-score 1.00
- Q5VWG9 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 3… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q5VWG9
- Elsewhere: RCSB PDB 5XMY · PDBe 5XMY · UniProt Q5VWG9
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