MolNFT v1 · #155418 · protein + DNA
Crystal structure of pluripotency reprogramming factor SOX17 mutant (SOX17EK) hmg domain bound to DNA
6L6Y · DNA (5'- D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)…: “Crystal structure of pluripotency reprogramming factor SOX17 mutant (SOX17EK) hmg domain bound to DNA”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability…
- PDB
- 6L6Y
- Type
- protein + DNA
- Length
- 224 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3'); DNA…
- UniProt
- Q61473
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (5'- D(P*GP*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*G)-3') | dna | 16 | — | — |
| B, E | DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)- 3') | dna | 16 | — | — |
| D, F | Transcription factor sox-17 | protein | 80 | 63% helix, 1% strand | Q61473 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, D, F
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 | 1039 | 0.83 | 0.84 | 69 | empty |
| 2 | 650 | 0.67 | 0.76 | 36 | SO4 |
| 3 | 94 | 0.42 | 0.79 | 12 | empty |
| 4 | 64 | 0.41 | 0.81 | 14 | empty |
| 5 | 62 | 0.28 | 0.74 | 10 | empty |
Interfaces
11 interfaces between chains.
- D–F · 740 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 705 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–D · 700 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–F · 700 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 678 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Compared structures
- 6L6Y · Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain… · the same entry in another collection · chain D against D, TM-score 1.00
- Q61473 · AlphaFold monomer V2.0 prediction for transcription factor sox-17 (Q61473) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q61473
- Elsewhere: RCSB PDB 6L6Y · PDBe 6L6Y · UniProt Q61473
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