MolNFT v1 · #114085 · protein + DNA
The mouse nucleosome structure containing H3T
5B1L · Histone H3T: “The mouse nucleosome structure containing H3T”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.76). MolNFT v1 #114085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B1L
- Type
- protein + DNA
- Length
- 1,043 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3T; Histone H4; Histone H2A type 1; Histone H2B type 3-a; DNA (146-mer)
- UniProt
- P62806, P22752, Q9D2U9
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3T | protein | 97 | 68% helix, 4% strand | — |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62806 |
| C | Histone H2A type 1 | protein | 108 | 55% helix, 6% strand | P22752 |
| D | Histone H2B type 3-a | protein | 93 | 75% helix, 4% strand | Q9D2U9 |
| F | Histone H4 | protein | 84 | 60% helix, 7% strand | P62806 |
| G | Histone H2A type 1 | protein | 104 | 58% helix, 6% strand | P22752 |
| H | Histone H2B type 3-a | protein | 92 | 76% helix, 4% strand | Q9D2U9 |
| I | DNA (146-mer) | dna | 145 | — | — |
| J | DNA (146-mer) | dna | 145 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 13 copies · chains C, D, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, G, H, I
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 | 390 | 0.76 | 0.86 | 46 | empty |
| 2 | 312 | 0.76 | 0.88 | 44 | empty |
| 3 | 242 | 0.72 | 0.87 | 34 | empty |
| 4 | 711 | 0.68 | 0.76 | 53 | MN |
| 5 | 157 | 0.68 | 0.88 | 30 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6438 Ų buried · 624 hydrogen bonds · nucleic-nucleic
- E–F · 2629 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2603 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2595 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2551 Ų buried · 22 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 P62806
- Every structure of UniProt P22752
- Every structure of UniProt Q9D2U9
- Elsewhere: RCSB PDB 5B1L · PDBe 5B1L · UniProt P62806 · UniProt P22752 · UniProt Q9D2U9
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