MolNFT v1 · #83150 · protein + DNA
Crystal structure of human nucleosome core particle lacking H3.1 N- terminal region
3W98 · Histone H3.1: “Crystal structure of human nucleosome core particle lacking H3.1 N- terminal region”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.77). MolNFT v1 #83150 on GenesisL1: 3D structure, binding sites…
- PDB
- 3W98
- Type
- protein + DNA
- Length
- 1,043 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; 146-mer DNA
- UniProt
- P68431, P62805, P04908, P06899
- Ligands
- MN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 68% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 76 | 67% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 106 | 55% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 95 | 73% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 99 | 67% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 84 | 61% helix, 7% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 57% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 91 | 76% helix, 4% strand | P06899 |
| I | 146-mer DNA | dna | 145 | — | — |
| J | 146-mer DNA | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains E, F
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 | 547 | 0.77 | 0.84 | 68 | empty |
| 2 | 534 | 0.76 | 0.83 | 50 | empty |
| 3 | 338 | 0.74 | 0.86 | 44 | empty |
| 4 | 774 | 0.69 | 0.76 | 62 | empty |
| 5 | 193 | 0.68 | 0.87 | 31 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6371 Ų buried · 515 hydrogen bonds · nucleic-nucleic
- E–F · 2651 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2637 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2570 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2534 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3W98 · Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region · the same entry in another collection · chain A against A, 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 3W98 · PDBe 3W98 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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