Research workbench
Crystal structure of human brachyury (T) G177D variant in complex with DNA
Analyse Crystal structure of human brachyury (T) G177D variant in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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