Research workbench
Structure of SNF2-nucleosome complex in ADP state
Analyse Structure of SNF2-nucleosome complex in ADP state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z3O
- Type
- protein + DNA
- Length
- 1,638 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (167-mer); Transcription…
- EC
- 3.6.4.-
- UniProt
- P84233, P62799, Q6AZJ8, P02281, P22082
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 66% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 87 | 59% helix, 5% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 53% helix, 2% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 71% helix, 2% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 68% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 86 | 55% helix, 5% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
| O | Transcription regulatory protein SNF2 (EC 3.6.4.-) | protein | 580 | 48% helix, 7% strand | P22082 |
Ligands and binding sites
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 | 1163 | 0.83 | 0.84 | 116 | ADP, MG |
| 2 | 1027 | 0.82 | 0.83 | 90 | empty |
| 3 | 557 | 0.78 | 0.84 | 75 | empty |
| 4 | 109 | 0.76 | 0.96 | 23 | empty |
| 5 | 1052 | 0.75 | 0.78 | 69 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6417 Ų buried · 397 hydrogen bonds · nucleic-nucleic
- C–D · 2518 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 2488 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2450 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2418 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P22082
- Elsewhere: RCSB PDB 5Z3O · PDBe 5Z3O · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P22082
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