MolNFT v1 · #114132 · protein + DNA
The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1.
5B31 · Histone H3.1: “The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1.”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #114132 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B31
- Type
- protein + DNA
- Length
- 1,042 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; Histone H2A.Z…
- UniProt
- P68431, P62805, P04908, P06899, P0C0S5
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 57% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 73% helix, 4% strand | P06899 |
| F | Histone H4 | protein | 83 | 60% helix, 7% strand | P62805 |
| G | Histone H2A.Z | protein | 104 | 57% helix, 6% strand | P0C0S5 |
| H | Histone H2B type 1-J | protein | 91 | 76% helix, 4% strand | P06899 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, E, F, I, J
- CL · Chloride ion · ion · 4 copies · chains A, C, D, J, E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.80 | 0.83 | 78 | empty |
| 2 | 435 | 0.75 | 0.85 | 42 | empty |
| 3 | 430 | 0.72 | 0.82 | 44 | empty |
| 4 | 769 | 0.71 | 0.78 | 72 | MN |
| 5 | 760 | 0.69 | 0.77 | 60 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6423 Ų buried · 606 hydrogen bonds · nucleic-nucleic
- G–H · 2648 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2615 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2597 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2492 Ų buried · 24 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt P0C0S5
- Elsewhere: RCSB PDB 5B31 · PDBe 5B31 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt P0C0S5
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