MolNFT v1 · #152930 · protein + DNA
Structure of SNF2-mmtv-a nucleosome complex at shl-2 in ADP state
6IY3 · Histone H3: “Structure of SNF2-mmtv-a nucleosome complex at shl-2 in ADP state”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.87). MolNFT v1 #152930 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6IY3
- Type
- protein + DNA
- Length
- 1,659 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (147-mer); Transcription regulatory…
- EC
- 3.6.4.-
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, A0A1L8FQA5, P22082
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 11 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 100 | 64% helix, 3% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 83 | 61% helix, 6% strand | P62799 |
| C | Histone H2A | protein | 111 | 52% helix, 5% strand | Q6AZJ8 |
| D | Histone H2B | protein | 98 | 71% helix, 4% strand | A0A1L8FQA5 |
| E | Histone H3 | protein | 99 | 64% helix, 4% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 88 | 57% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 109 | 52% helix, 4% strand | Q6AZJ8 |
| H | Histone H2B | protein | 97 | 71% helix, 2% strand | A0A1L8FQA5 |
| J | DNA (147-mer) | dna | 147 | — | — |
| I | DNA (147-mer) | dna | 147 | — | — |
| O | Transcription regulatory protein SNF2 (EC 3.6.4.-) | protein | 580 | 46% helix, 6% 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 | 938 | 0.87 | 0.89 | 110 | empty |
| 2 | 765 | 0.81 | 0.84 | 76 | empty |
| 3 | 640 | 0.78 | 0.84 | 69 | empty |
| 4 | 484 | 0.78 | 0.85 | 71 | empty |
| 5 | 432 | 0.74 | 0.84 | 49 | empty |
Interfaces
42 interfaces between chains.
- J–I · 6420 Ų buried · 528 hydrogen bonds · nucleic-nucleic
- G–H · 2673 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2649 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 2525 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6IY3 · Structure of Snf2-MMTV-A nucleosome complex at shl-2 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 6IY3 · PDBe 6IY3 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt A0A1L8FQA5 · UniProt P22082
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