MolNFT v1 · #151616 · protein + DNA
OCT4/SOX2:UTF1 structure
6HT5 · DNA (5'- D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP…: “OCT4/SOX2:UTF1 structure”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #151616 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HT5
- Type
- protein + DNA
- Length
- 221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G) -3'); DNA…
- UniProt
- P48432, P20263
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G) -3') | dna | 22 | — | — |
| B | DNA (5'- D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)- 3') | dna | 21 | — | — |
| D | Transcription factor sox-2 | protein | 77 | 65% helix, 0% strand | P48432 |
| E | Pou domain, class 5, transcription factor 1 | protein | 101 | 79% helix, 0% strand | P20263 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.69 | 0.88 | 30 | empty |
| 2 | 214 | 0.43 | 0.73 | 17 | empty |
| 3 | 68 | 0.31 | 0.75 | 14 | empty |
| 4 | 54 | 0.26 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 905 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–D · 856 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 766 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–E · 345 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 331 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6HT5 · Oct4/Sox2:UTF1 structure · the same entry in another collection · chain A against A, TM-score 1.00
- P48432 · AlphaFold monomer V2.0 prediction for transcription factor sox-2 (P48432) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P20263 · AlphaFold monomer V2.0 prediction for pou domain, class 5, transcription factor 1 (P20263) · a predicted model of the same protein · chain E against A, TM-score 0.74
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 P48432
- Every structure of UniProt P20263
- Elsewhere: RCSB PDB 6HT5 · PDBe 6HT5 · UniProt P48432 · UniProt P20263
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