Research workbench
OCT4-SOX2-bound nucleosome - shl-6
Analyse OCT4-SOX2-bound nucleosome - shl-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T90
- Type
- protein + DNA
- Length
- 1,185 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (146-mer)…
- UniProt
- P68431, P62805, P04908, P06899, P42212, Q01860, P48431
- Ligands
- PTD
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 11 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 94 | 70% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 82 | 60% helix, 7% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 109 | 53% helix, 6% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 93 | 74% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 95 | 69% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 81 | 60% helix, 7% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 109 | 51% helix, 6% strand | P04908 |
| I | DNA (146-mer) | dna | 141 | — | — |
| J | DNA (146-mer) | dna | 141 | — | — |
| K | Green fluorescent PROTEIN,POU domain, class 5, transcription factor 1 | protein | 73 | 78% helix, 0% strand | P42212, Q01860 |
| L | Transcription factor sox-2 | protein | 74 | 68% helix, 0% strand | P48431 |
Ligands and binding sites
- PTD · Pentanedial · ligand · 9 copies · chains A, E, B, C, H, D, F, G, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.79 | 0.81 | 104 | PTD |
| 2 | 173 | 0.75 | 0.92 | 28 | empty |
| 3 | 620 | 0.73 | 0.81 | 53 | empty |
| 4 | 376 | 0.72 | 0.84 | 39 | empty |
| 5 | 719 | 0.70 | 0.78 | 49 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6310 Ų buried · 473 hydrogen bonds · nucleic-nucleic
- G–H · 2651 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2634 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2560 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2558 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 covalent (covalent ligand).
Compared structures
- 6T90 · OCT4-SOX2-bound nucleosome - SHL-6 · the same entry in another collection · chain L against L, TM-score 1.00
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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt P42212
- Every structure of UniProt Q01860
- Every structure of UniProt P48431
- Elsewhere: RCSB PDB 6T90 · PDBe 6T90 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P42212 · UniProt Q01860 · UniProt P48431
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