Research workbench
Nucleosome with tbp and tfiia bound at shl -6
Analyse Nucleosome with tbp and tfiia bound at shl -6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OH9
- Type
- protein + DNA
- Length
- 1,434 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (145-mer); Tata-binding…
- UniProt
- P84233, P62799, Q6AZJ8, P02281, G4XSG8, P32773, A0A6A5PRZ0
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 13 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 68% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 60% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 109 | 56% helix, 6% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 97 | 72% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 98 | 64% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 80 | 58% helix, 9% strand | P62799 |
| G | Histone H2A | protein | 106 | 55% helix, 7% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 75% helix, 4% strand | P02281 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K | Tata-binding protein | protein | 180 | 27% helix, 36% strand | G4XSG8 |
| L | Transcription initiation factor iia large subunit | protein | 96 | 36% helix, 34% strand | P32773 |
| M | Transcription initiation factor iia subunit 2 | protein | 104 | 39% helix, 40% strand | A0A6A5PRZ0 |
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 | 838 | 0.81 | 0.84 | 91 | empty |
| 2 | 165 | 0.79 | 0.94 | 26 | empty |
| 3 | 101 | 0.77 | 0.98 | 28 | empty |
| 4 | 438 | 0.75 | 0.85 | 50 | empty |
| 5 | 379 | 0.73 | 0.84 | 45 | empty |
Interfaces
46 interfaces between chains.
- I–J · 6481 Ų buried · 521 hydrogen bonds · nucleic-nucleic
- C–D · 2658 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2592 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2543 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2528 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7OH9 · Nucleosome with TBP and TFIIA bound at SHL -6 · the same entry in another collection · chain M against M, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt G4XSG8
- Every structure of UniProt P32773
- Every structure of UniProt A0A6A5PRZ0
- Elsewhere: RCSB PDB 7OH9 · PDBe 7OH9 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt G4XSG8 · UniProt P32773 · UniProt A0A6A5PRZ0
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