Research workbench
Human-D02 nucleosome core particle with biotin-streptavidin label
Analyse Human-D02 nucleosome core particle with biotin-streptavidin label in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R0C
- Type
- protein + DNA
- Length
- 1,031 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; DNA (142-mer)
- UniProt
- P84243, P62805, P0C0S8, P62807
- Ligands
- MN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 8 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.3 | protein | 97 | 68% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 83 | 61% helix, 7% strand | P62805 |
| C | Histone H2A type 1 | protein | 103 | 54% helix, 4% strand | P0C0S8 |
| D, H | Histone H2B type 1-C/E/F/G/I | protein | 93 | 75% helix, 2% strand | P62807 |
| F | Histone H4 | protein | 76 | 66% helix, 8% strand | P62805 |
| G | Histone H2A type 1 | protein | 105 | 54% helix, 3% strand | P0C0S8 |
| I | DNA (142-mer) | dna | 142 | — | — |
| J | DNA (142-mer) | dna | 142 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, B
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 | 1004 | 0.78 | 0.80 | 88 | empty |
| 2 | 511 | 0.76 | 0.84 | 52 | empty |
| 3 | 436 | 0.70 | 0.81 | 41 | empty |
| 4 | 312 | 0.70 | 0.84 | 32 | empty |
| 5 | 415 | 0.69 | 0.81 | 48 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6338 Ų buried · 550 hydrogen bonds · nucleic-nucleic
- C–D · 2583 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2570 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2520 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2411 Ų buried · 18 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 P84243
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Elsewhere: RCSB PDB 6R0C · PDBe 6R0C · UniProt P84243 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807
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