MolNFT v1 · #148392 · protein + DNA
Crystal structure of human brachyury (T) G177D variant in complex with DNA
6F59 · DNA (26-mer): “Crystal structure of human brachyury (T) G177D variant in complex with DNA”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.60). MolNFT v1 #148392 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6F59
- Type
- protein + DNA
- Length
- 415 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (26-mer); Brachyury protein
- UniProt
- O15178
- Ligands
- NA
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (26-mer) | dna | 26 | — | — |
| A | Brachyury protein | protein | 178 | 22% helix, 35% strand | O15178 |
| B | Brachyury protein | protein | 185 | 22% helix, 34% strand | O15178 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.60 | 0.79 | 34 | empty |
| 2 | 322 | 0.59 | 0.78 | 36 | empty |
| 3 | 213 | 0.47 | 0.74 | 24 | empty |
| 4 | 70 | 0.33 | 0.75 | 18 | empty |
| 5 | 64 | 0.27 | 0.73 | 9 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1129 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- D–B · 583 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 581 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–B · 519 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 513 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6F59 · Crystal structure of human Brachyury (T) G177D variant in complex with DNA · the same entry in another collection · chain C against C, TM-score 1.00
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 O15178
- Elsewhere: RCSB PDB 6F59 · PDBe 6F59 · UniProt O15178
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