MolNFT v1 · #164733 · protein + DNA
Structure of human SOX11 transcription factor in complex with a nucleosome
6T7D · Histone H3.2: “Structure of human SOX11 transcription factor in complex with a nucleosome”. Electron microscopy, 20 pockets (best druggability 0.62). MolNFT v1 #164733 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6T7D
- Type
- protein + DNA
- Length
- 1,087 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 (151-mer)…
- UniProt
- Q71DI3, P62805, P04908, O60814, P35716
- Pockets
- 20 · best druggability 0.62
Structure
electron microscopy · 9 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 64% helix, 4% strand | Q71DI3 |
| B | Histone H4 | protein | 84 | 58% helix, 6% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 110 | 45% helix, 5% strand | P04908 |
| D, H | Histone H2B type 1-K | protein | 95 | 73% helix, 4% strand | O60814 |
| E | Histone H3.2 | protein | 97 | 64% helix, 4% strand | Q71DI3 |
| F | Histone H4 | protein | 87 | 55% helix, 6% strand | P62805 |
| I | DNA (151-mer) | dna | 117 | — | — |
| J | DNA (151-mer) | dna | 117 | — | — |
| K | Transcription factor sox-11 | protein | 77 | 65% helix, 0% strand | P35716 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.62 | 0.76 | 61 | empty |
| 2 | 583 | 0.59 | 0.73 | 86 | empty |
| 3 | 569 | 0.58 | 0.73 | 78 | empty |
| 4 | 400 | 0.58 | 0.76 | 41 | empty |
| 5 | 465 | 0.58 | 0.74 | 48 | empty |
Interfaces
30 interfaces between chains.
- I–J · 5292 Ų buried · 458 hydrogen bonds · nucleic-nucleic
- C–D · 403 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 385 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 381 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 373 Ų buried · 3 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 P35716
- Elsewhere: RCSB PDB 6T7D · PDBe 6T7D · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P35716
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