Research workbench
Structure of human SOX2 transcription factor in complex with a nucleosome
Analyse Structure of human SOX2 transcription factor in complex with a nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T7B
- Type
- protein + DNA
- Length
- 1,028 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (147-mer)…
- UniProt
- Q71DI3, P62805, P04908, O60814, P48431
- Pockets
- 20 · best druggability 0.64
Structure
electron microscopy · 9 distinct chains · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 62% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 84 | 58% helix, 7% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 106 | 47% helix, 4% strand | P04908 |
| D, H | Histone H2B type 1-K | protein | 95 | 72% helix, 2% strand | O60814 |
| E | Histone H3.2 | protein | 97 | 63% helix, 2% strand | Q71DI3 |
| F | Histone H4 | protein | 81 | 60% helix, 5% strand | P62805 |
| I | DNA (147-mer) | dna | 95 | — | — |
| J | DNA (147-mer) | dna | 95 | — | — |
| K | Transcription factor sox-2 | protein | 76 | 64% helix, 0% strand | P48431 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.64 | 0.74 | 83 | empty |
| 2 | 564 | 0.64 | 0.76 | 108 | empty |
| 3 | 302 | 0.61 | 0.80 | 34 | empty |
| 4 | 438 | 0.61 | 0.77 | 69 | empty |
| 5 | 241 | 0.60 | 0.81 | 28 | empty |
Interfaces
31 interfaces between chains.
- I–J · 4181 Ų buried · 309 hydrogen bonds · nucleic-nucleic
- C–D · 457 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 433 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 420 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Every structure of UniProt P48431
- Elsewhere: RCSB PDB 6T7B · PDBe 6T7B · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P48431
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