Research workbench
The motor-nucleosome module of human chromatin remodeling pbaf- nucleosome complex
Analyse The motor-nucleosome module of human chromatin remodeling pbaf- nucleosome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VDT
- Type
- protein + DNA
- Length
- 1,656 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of transcription activator BRG1; Histone H4; Histone H2A; Histone H2B 1.1…
- EC
- 3.6.4.-
- UniProt
- P51532, P62799, Q6AZJ8, P02281, A0A310TTQ1
- Ligands
- BEF, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of transcription activator BRG1 (EC 3.6.4.-) | protein | 617 | 44% helix, 9% strand | P51532 |
| B | Histone H4 | protein | 87 | 63% helix, 7% strand | P62799 |
| C | Histone H2A | protein | 107 | 53% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| E | Histone H3 | protein | 95 | 65% helix, 3% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 86 | 57% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 108 | 53% helix, 6% strand | Q6AZJ8 |
| I | DNA (207-mer) | dna | 135 | — | — |
| J | DNA (207-mer) | dna | 137 | — | — |
| K | Histone H3 | protein | 98 | 60% helix, 4% strand | A0A310TTQ1 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
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 | 776 | 0.85 | 0.88 | 80 | empty |
| 2 | 1035 | 0.80 | 0.81 | 90 | empty |
| 3 | 790 | 0.75 | 0.80 | 77 | empty |
| 4 | 421 | 0.75 | 0.85 | 49 | empty |
| 5 | 454 | 0.74 | 0.84 | 52 | empty |
Interfaces
42 interfaces between chains.
- I–J · 6267 Ų buried · 742 hydrogen bonds · nucleic-nucleic
- G–H · 2596 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2579 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2567 Ų buried · 16 hydrogen bonds · protein-protein
- B–K · 2434 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7VDT · The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex · the same entry in another collection · chain K against K, TM-score 1.00
- P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P51532
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt A0A310TTQ1
- Elsewhere: RCSB PDB 7VDT · PDBe 7VDT · UniProt P51532 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt A0A310TTQ1
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