MolNFT v1 · #154146 · protein + DNA
Human nucleosome core particle with GAMMAH2A.X variant
6K1I · Histone H3.1: “Human nucleosome core particle with GAMMAH2A.X variant”. X-ray diffraction, 3 ligands (MN, K, CL), 20 pockets (best druggability 0.80). MolNFT v1 #154146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6K1I
- Type
- protein + DNA
- Length
- 1,069 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2AX; Histone H2B type 1-J; DNA (147-mer)
- UniProt
- P68431, P62805, P16104, P06899
- Ligands
- MN, K, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 98 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 80 | 63% helix, 8% strand | P62805 |
| C, G | Histone H2AX | protein | 110 | 54% helix, 6% strand | P16104 |
| D | Histone H2B type 1-J | protein | 97 | 72% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62805 |
| H | Histone H2B type 1-J | protein | 96 | 73% helix, 4% strand | P06899 |
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 23 copies · chains E, F, I, J
- K · Potassium ion · metal · 2 copies · chains I, J
- CL · Chloride ion · ion · 2 copies · chains C, D, 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 | 1078 | 0.80 | 0.81 | 84 | empty |
| 2 | 597 | 0.73 | 0.81 | 49 | empty |
| 3 | 463 | 0.70 | 0.81 | 48 | empty |
| 4 | 721 | 0.69 | 0.77 | 41 | empty |
| 5 | 797 | 0.68 | 0.76 | 63 | MN |
Interfaces
36 interfaces between chains.
- I–J · 6573 Ų buried · 677 hydrogen bonds · nucleic-nucleic
- E–F · 2667 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2645 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2592 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2555 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 P16104
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6K1I · PDBe 6K1I · UniProt P68431 · UniProt P62805 · UniProt P16104 · UniProt P06899
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