MolNFT v1 · #140111 · protein + DNA
Crystal structure of the human nucleosome at 2.09 ångström resolution
5Y0C · DNA (146-mer): “Crystal structure of the human nucleosome at 2.09 ångström resolution”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.82). MolNFT v1 #140111 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Y0C
- Type
- protein + DNA
- Length
- 1,045 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (146-mer); Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J
- UniProt
- P68431, P62805, P04908, P06899
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (146-mer) | dna | 145 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
| A | Histone H3.1 | protein | 96 | 67% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 77 | 64% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 108 | 55% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 92 | 75% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 65% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 57% helix, 7% strand | P04908 |
| H | Histone H2B type 1-J | protein | 91 | 76% helix, 4% strand | P06899 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 10 copies · chains I, J, E
- CL · Chloride ion · ion · 4 copies · chains A, J, C, D, E, I, G, H
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 | 1169 | 0.82 | 0.84 | 109 | empty |
| 2 | 472 | 0.75 | 0.84 | 47 | empty |
| 3 | 338 | 0.73 | 0.85 | 44 | empty |
| 4 | 674 | 0.70 | 0.78 | 57 | MN |
| 5 | 869 | 0.69 | 0.76 | 73 | MN |
Interfaces
36 interfaces between chains.
- I–J · 6468 Ų buried · 611 hydrogen bonds · nucleic-nucleic
- E–F · 2658 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2617 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2571 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2557 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5Y0C · Crystal Structure of the human nucleosome at 2.09 angstrom resolution · the same entry in another collection · chain I against I, TM-score 1.00
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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 5Y0C · PDBe 5Y0C · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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