MolNFT v1 · #141334 · protein + DNA
Structure of SNF2-nucleosome complex at shl-2 in ADP befx state
5Z3V · Transcription regulatory protein SNF2: “Structure of SNF2-nucleosome complex at shl-2 in ADP befx state”. Electron microscopy, 3 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.83). MolNFT v1 #141334 on GenesisL1: 3D…
- PDB
- 5Z3V
- Type
- protein + DNA
- Length
- 1,631 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription regulatory protein SNF2; Histone H3.2; Histone H4; Histone H2A; Histone H2B…
- EC
- 3.6.4.-
- UniProt
- P22082, P84233, P62799, Q6AZJ8, P02281
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Transcription regulatory protein SNF2 (EC 3.6.4.-) | protein | 576 | 47% helix, 7% strand | P22082 |
| A | Histone H3.2 | protein | 98 | 64% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 62% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 55% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 66% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 88 | 58% helix, 8% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains O
- BEF · Beryllium trifluoride ion · ligand · chains O
- MG · Magnesium ion · metal · 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 | 996 | 0.83 | 0.84 | 96 | empty |
| 2 | 780 | 0.82 | 0.84 | 74 | empty |
| 3 | 840 | 0.81 | 0.84 | 75 | empty |
| 4 | 1162 | 0.76 | 0.79 | 103 | empty |
| 5 | 416 | 0.75 | 0.85 | 54 | ADP, BEF, MG |
Interfaces
39 interfaces between chains.
- I–J · 6509 Ų buried · 432 hydrogen bonds · nucleic-nucleic
- G–H · 2574 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2556 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2529 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2487 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5Z3V · Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state · the same entry in another collection · chain J against J, 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 P22082
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 5Z3V · PDBe 5Z3V · UniProt P22082 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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