MolNFT v1 · #148391 · protein + DNA
Crystal structure of human brachyury (T) in complex with DNA
6F58 · DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*…: “Crystal structure of human brachyury (T) in complex with DNA”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.60). MolNFT v1 #148391 on GenesisL1: 3D…
- PDB
- 6F58
- Type
- protein + DNA
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP* TP*T)-3')…
- UniProt
- O15178
- Ligands
- NA
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP* TP*T)-3') | dna | 23 | — | — |
| D | DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP* TP*T)-3') | dna | 24 | — | — |
| A | Brachyury protein | protein | 180 | 21% helix, 37% strand | O15178 |
| B | Brachyury protein | protein | 175 | 19% helix, 37% strand | O15178 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.60 | 0.79 | 36 | empty |
| 2 | 270 | 0.59 | 0.79 | 32 | empty |
| 3 | 96 | 0.33 | 0.74 | 12 | empty |
| 4 | 55 | 0.29 | 0.75 | 16 | empty |
| 5 | 50 | 0.27 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1009 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- D–B · 578 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–A · 565 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 514 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–B · 513 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6F58 · Crystal structure of human Brachyury (T) 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 6F58 · PDBe 6F58 · UniProt O15178
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