Research workbench
Structural basis of gene regulation by the grainyhead transcription factor superfamily
Analyse Structural basis of gene regulation by the grainyhead transcription factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MPF
- Type
- protein + DNA
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Grainyhead-like protein 1 homolog; DNA (5'-D(*AP*AP*AP*AP*CP*CP*GP*GP*TP*TP*TP*T)-3')
- UniProt
- Q9NZI5
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Grainyhead-like protein 1 homolog | protein | 196 | 14% helix, 39% strand | Q9NZI5 |
| B | Grainyhead-like protein 1 homolog | protein | 202 | 16% helix, 38% strand | Q9NZI5 |
| E, F | DNA (5'-D(*AP*AP*AP*AP*CP*CP*GP*GP*TP*TP*TP*T)-3') | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.65 | 0.96 | 21 | empty |
| 2 | 477 | 0.65 | 0.77 | 44 | empty |
| 3 | 250 | 0.55 | 0.77 | 32 | empty |
| 4 | 81 | 0.40 | 0.78 | 15 | empty |
| 5 | 87 | 0.32 | 0.74 | 23 | empty |
Interfaces
6 interfaces between chains.
- E–F · 508 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- B–F · 404 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 395 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–E · 331 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–F · 323 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5MPF · Structural Basis of Gene Regulation by the Grainyhead Transcription Factor Superfamily · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZI5 · AlphaFold monomer V2.0 prediction for grainyhead-like protein 1 homolog (Q9NZI5) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9NZI5
- Elsewhere: RCSB PDB 5MPF · PDBe 5MPF · UniProt Q9NZI5
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