Research workbench
Crystal structure of pluripotency reprogramming factor SOX17 mutant (SOX17EK) hmg domain bound to DNA
Analyse Crystal structure of pluripotency reprogramming factor SOX17 mutant (SOX17EK)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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