Research workbench
Crystal structure of the dm domain of human DMRT1 bound to 25MER target DNA
Analyse Crystal structure of the dm domain of human DMRT1 bound to 25MER target DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YJ0
- Type
- protein + DNA
- Length
- 238 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Doublesex- and mab-3-related transcription factor 1; DNA (25-mer)
- UniProt
- Q9Y5R6
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Doublesex- and mab-3-related transcription factor 1 | protein | 62 | 44% helix, 0% strand | Q9Y5R6 |
| B, C | Doublesex- and mab-3-related transcription factor 1 | protein | 63 | 57% helix, 3% strand | Q9Y5R6 |
| D | DNA (25-mer) | dna | 25 | — | — |
| E | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.69 | 0.85 | 41 | empty |
| 2 | 403 | 0.67 | 0.80 | 40 | empty |
| 3 | 314 | 0.56 | 0.76 | 28 | empty |
| 4 | 111 | 0.40 | 0.76 | 20 | empty |
| 5 | 69 | 0.34 | 0.77 | 14 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1128 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–B · 683 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 630 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 623 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 540 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4YJ0 · Crystal structure of the DM domain of human DMRT1 bound to 25mer target DNA · the same entry in another collection · chain E against E, TM-score 1.00
- Q9Y5R6 · AlphaFold monomer V2.0 prediction for doublesex- and mab-3-related transcription factor 1… · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q9Y5R6
- Elsewhere: RCSB PDB 4YJ0 · PDBe 4YJ0 · UniProt Q9Y5R6
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