MolNFT v1 · #84059 · protein + DNA
Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2AA and H2BA
3X1T · DNA (146-mer): “Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2AA and…”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.79). MolNFT v1 #84059 on…
- PDB
- 3X1T
- Type
- protein + DNA
- Length
- 1,053 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; Histone H2B type 1-a
- UniProt
- P68431, P62805, Q8CGP4, P70696
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | DNA (146-mer) | dna | 146 | — | — |
| A, E | Histone H3.1 | protein | 98 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 81 | 60% helix, 9% strand | P62805 |
| C | Histone H2A | protein | 105 | 57% helix, 7% strand | Q8CGP4 |
| D, H | Histone H2B type 1-a | protein | 93 | 74% helix, 4% strand | P70696 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62805 |
| G | Histone H2A | protein | 106 | 57% helix, 7% strand | Q8CGP4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 22 copies · chains I, J, A, C, D, G, H
- CL · Chloride ion · ion · 8 copies · chains J, I, B, C, D
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 | 791 | 0.79 | 0.83 | 79 | empty |
| 2 | 432 | 0.77 | 0.86 | 58 | empty |
| 3 | 503 | 0.77 | 0.85 | 61 | CL |
| 4 | 595 | 0.70 | 0.79 | 66 | empty |
| 5 | 339 | 0.66 | 0.81 | 36 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6428 Ų buried · 555 hydrogen bonds · nucleic-nucleic
- E–F · 2686 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2640 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2621 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2565 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3X1T · Crystal structure of nucleosome core particle consisting of mouse testis specific histone… · the same entry in another collection · chain H against H, TM-score 1.00
- P70696 · AlphaFold monomer V2.0 prediction for histone H2B type 1-a (P70696) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q8CGP4
- Every structure of UniProt P70696
- Elsewhere: RCSB PDB 3X1T · PDBe 3X1T · UniProt P68431 · UniProt P62805 · UniProt Q8CGP4 · UniProt P70696
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.