MolNFT v1 · #164728 · protein + DNA
Structure of human SOX11 transcription factor in complex with a short DNA fragment
6T78 · Transcription factor sox-11: “Structure of human SOX11 transcription factor in complex with a short DNA fragment”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #164728 on GenesisL1: 3D structure, binding sites…
- PDB
- 6T78
- Type
- protein + DNA
- Length
- 201 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor sox-11; DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)…
- UniProt
- P35716
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 6 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor sox-11 | protein | 77 | 65% helix, 0% strand | P35716 |
| B | Transcription factor sox-11 | protein | 74 | 69% helix, 0% strand | P35716 |
| C | DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)- 3') | dna | 13 | — | — |
| D | DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)- 3') | dna | 13 | — | — |
| F | DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)- 3') | dna | 12 | — | — |
| G | DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)- 3') | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.59 | 0.78 | 23 | empty |
| 2 | 292 | 0.59 | 0.78 | 25 | empty |
| 3 | 200 | 0.57 | 0.80 | 28 | empty |
| 4 | 147 | 0.55 | 0.82 | 21 | empty |
| 5 | 60 | 0.31 | 0.76 | 9 | empty |
Interfaces
15 interfaces between chains.
- B–C · 730 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 719 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–G · 682 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 654 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 570 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 6T78 · Structure of human Sox11 transcription factor in complex with a short DNA fragment · the same entry in another collection · chain G against G, TM-score 1.00
- P35716 · AlphaFold monomer V2.0 prediction for transcription factor sox-11 (P35716) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P35716
- Elsewhere: RCSB PDB 6T78 · PDBe 6T78 · UniProt P35716
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