MolNFT v1 · #189391 · protein + DNA
The overall structure of human chromatin remodeling pbaf-nucleosome complex
7VDV · Histone H4: “The overall structure of human chromatin remodeling pbaf-nucleosome complex”. Electron microscopy, 3 ligands (BEF, ADP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #189391 on GenesisL1: 3D structure, binding…
- PDB
- 7VDV
- Type
- protein + DNA
- Length
- 4,548 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H4; Histone H2A; Histone H2B 1.1; Histone H3; DNA (207-mer); Isoform 2 of…
- EC
- 3.6.4.-
- UniProt
- P62799, Q6AZJ8, P02281, A0A310TTQ1, P51532, O96019, P60709, Q68CP9, Q8WUB8, Q9NPI1, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q86U86
- Ligands
- BEF, ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 23 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Histone H4 | protein | 87 | 57% helix, 7% strand | P62799 |
| C | Histone H2A | protein | 107 | 53% helix, 6% 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 | 58% helix, 6% strand | P62799 |
| G | Histone H2A | protein | 108 | 54% helix, 6% strand | Q6AZJ8 |
| I | DNA (207-mer) | dna | 135 | — | — |
| J | DNA (207-mer) | dna | 137 | — | — |
| A | Isoform 2 of transcription activator BRG1 (EC 3.6.4.-) | protein | 809 | 53% helix, 7% strand | P51532 |
| N | Actin-like protein 6A | protein | 334 | 38% helix, 17% strand | O96019 |
| P | Actin, cytoplasmic 1 | protein | 317 | 42% helix, 15% strand | P60709 |
| Q | At-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2 | protein | 500 | 58% helix, 2% strand | Q68CP9 |
| R | Phd finger protein 10 | protein | 92 | 33% helix, 7% strand | Q8WUB8 |
| T | Isoform 2 of bromodomain-containing protein 7 | protein | 267 | 51% helix, 1% strand | Q9NPI1 |
| U | Unknown | protein | 7 | 0% helix, 0% strand | — |
| V | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 | protein | 238 | 45% helix, 17% strand | Q12824 |
| W | SWI/SNF complex subunit SMARCC2 | protein | 248 | 69% helix, 0% strand | Q8TAQ2 |
| X | SWI/SNF complex subunit SMARCC2 | protein | 252 | 59% helix, 2% strand | Q8TAQ2 |
| Y | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 | protein | 245 | 62% helix, 5% strand | Q96GM5 |
| Z | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 | protein | 92 | 72% helix, 0% strand | Q969G3 |
| a | Protein polybromo-1 | protein | 92 | 47% helix, 1% strand | Q86U86 |
| K | Histone H3 | protein | 98 | 65% helix, 4% strand | A0A310TTQ1 |
| M | Unknown | protein | 16 | 88% helix, 0% strand | — |
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 | 909 | 0.86 | 0.87 | 97 | empty |
| 2 | 1079 | 0.84 | 0.85 | 114 | empty |
| 3 | 763 | 0.84 | 0.88 | 77 | empty |
| 4 | 939 | 0.84 | 0.85 | 77 | empty |
| 5 | 891 | 0.84 | 0.85 | 88 | empty |
Interfaces
94 interfaces between chains.
- I–J · 6214 Ų buried · 855 hydrogen bonds · nucleic-nucleic
- G–H · 2577 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2537 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2529 Ų buried · 18 hydrogen bonds · protein-protein
- B–K · 2340 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7VDV · The overall structure of human chromatin remodeling PBAF-nucleosome complex · the same entry in another collection · chain N against N, 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 P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt A0A310TTQ1
- Every structure of UniProt P51532
- Every structure of UniProt O96019
- Every structure of UniProt P60709
- Every structure of UniProt Q68CP9
- Every structure of UniProt Q8WUB8
- Every structure of UniProt Q9NPI1
- Every structure of UniProt Q12824
- Every structure of UniProt Q8TAQ2
- Every structure of UniProt Q96GM5
- Every structure of UniProt Q969G3
- Every structure of UniProt Q86U86
- Elsewhere: RCSB PDB 7VDV · PDBe 7VDV · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt A0A310TTQ1 · UniProt P51532 · UniProt O96019 · UniProt P60709 · UniProt Q68CP9 · UniProt Q8WUB8 · UniProt Q9NPI1 · UniProt Q12824 · UniProt Q8TAQ2 · UniProt Q96GM5 · UniProt Q969G3 · UniProt Q86U86
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