MolNFT v1 · #152929 · protein + DNA
Structure of SNF2-mmtv-a nucleosome complex at SHL2 in ADP state
6IY2 · Histone H3: “Structure of SNF2-mmtv-a nucleosome complex at SHL2 in ADP state”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #152929 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6IY2
- Type
- protein + DNA
- Length
- 1,661 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (167-mer); DNA (147-mer)…
- EC
- 3.6.4.-
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, A0A1L8FQA5, P22082
- 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 | protein | 100 | 64% helix, 3% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 88 | 53% helix, 5% strand | P62799 |
| C | Histone H2A | protein | 111 | 51% helix, 6% strand | Q6AZJ8 |
| D | Histone H2B | protein | 100 | 69% helix, 4% strand | A0A1L8FQA5 |
| E | Histone H3 | protein | 99 | 64% helix, 3% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 81 | 63% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 111 | 47% helix, 5% strand | Q6AZJ8 |
| H | Histone H2B | protein | 97 | 73% helix, 4% strand | A0A1L8FQA5 |
| J | DNA (167-mer) | dna | 147 | — | — |
| I | DNA (147-mer) | dna | 147 | — | — |
| O | Transcription regulatory protein SNF2 (EC 3.6.4.-) | protein | 580 | 45% helix, 8% strand | P22082 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains O
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 | 883 | 0.86 | 0.88 | 96 | empty |
| 2 | 903 | 0.82 | 0.84 | 71 | empty |
| 3 | 409 | 0.80 | 0.88 | 56 | empty |
| 4 | 448 | 0.77 | 0.86 | 60 | empty |
| 5 | 360 | 0.75 | 0.86 | 45 | empty |
Interfaces
41 interfaces between chains.
- J–I · 6421 Ų buried · 471 hydrogen bonds · nucleic-nucleic
- G–H · 2702 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2673 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2536 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2530 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6IY2 · Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state · the same entry in another collection · chain O against O, TM-score 1.00
- P22082 · AlphaFold monomer V2.0 prediction for transcription regulatory protein SNF2 (P22082) · a predicted model of the same protein · chain O 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt A0A1L8FQA5
- Every structure of UniProt P22082
- Elsewhere: RCSB PDB 6IY2 · PDBe 6IY2 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQA5 · UniProt P22082
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