MolNFT v1 · #157898 · protein + DNA
Cryo-EM structure of singly-bound SNF2H-nucleosome complex with SNF2H bound at shl-2
6NE3 · Histone H3.2: “Cryo-EM structure of singly-bound SNF2H-nucleosome complex with SNF2H bound at shl-2”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #157898 on GenesisL1: 3D structure, binding…
- PDB
- 6NE3
- Type
- protein + DNA
- Length
- 1,557 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B; DNA (156-mer); SWI/SNF-related…
- EC
- 3.6.4.-
- UniProt
- P84233, P62799, P06897, A0A1L8FQ56, O60264
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 99 | 63% helix, 2% strand | P84233 |
| B | Histone H4 | protein | 88 | 55% helix, 5% strand | P62799 |
| C | Histone H2A type 1 | protein | 114 | 46% helix, 4% strand | P06897 |
| D | Histone H2B | protein | 99 | 70% helix, 4% strand | A0A1L8FQ56 |
| E | Histone H3.2 | protein | 99 | 62% helix, 3% strand | P84233 |
| F | Histone H4 | protein | 83 | 59% helix, 5% strand | P62799 |
| G | Histone H2A type 1 | protein | 109 | 50% helix, 4% strand | P06897 |
| H | Histone H2B | protein | 93 | 74% helix, 2% strand | A0A1L8FQ56 |
| J | DNA (156-mer) | dna | 156 | — | — |
| I | DNA (156-mer) | dna | 156 | — | — |
| W | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (EC 3.6.4.-) | protein | 461 | 45% helix, 11% strand | O60264 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains W
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 | 642 | 0.86 | 0.91 | 80 | empty |
| 2 | 809 | 0.80 | 0.83 | 76 | empty |
| 3 | 949 | 0.77 | 0.80 | 68 | empty |
| 4 | 445 | 0.76 | 0.85 | 43 | empty |
| 5 | 449 | 0.74 | 0.84 | 44 | empty |
Interfaces
41 interfaces between chains.
- J–I · 7115 Ų buried · 674 hydrogen bonds · nucleic-nucleic
- C–D · 2648 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2612 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2573 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2451 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6NE3 · Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 · the same entry in another collection · chain W against W, TM-score 1.00
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain G against A, TM-score 0.93
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 P06897
- Every structure of UniProt A0A1L8FQ56
- Every structure of UniProt O60264
- Elsewhere: RCSB PDB 6NE3 · PDBe 6NE3 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt A0A1L8FQ56 · UniProt O60264
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