MolNFT v1 · #111175 · protein + DNA
Crystal structure of the dm domain of human DMRT1 bound to 25MER target DNA
4YJ0 · Doublesex- and mab-3-related transcription factor 1: “Crystal structure of the dm domain of human DMRT1 bound to 25MER target DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.69). MolNFT v1 #111175 on…
- 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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