MolNFT v1 · #177127 · protein + DNA
NSD2 E1099K mutant bound to nucleosome
7E8D · Histone H3.1: “NSD2 E1099K mutant bound to nucleosome”. Electron microscopy, 2 ligands (SFG, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #177127 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E8D
- Type
- protein + DNA
- Length
- 1,327 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1; Histone H2B type 1-J; DNA (185-mer)…
- EC
- 2.1.1.357
- UniProt
- P68431, P62805, P0C0S8, P06899, O96028
- Ligands
- SFG, ZN
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 10 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 66% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 79 | 63% helix, 8% strand | P62805 |
| C, G | Histone H2A type 1 | protein | 109 | 52% helix, 6% strand | P0C0S8 |
| D | Histone H2B type 1-J | protein | 94 | 72% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 104 | 61% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 78 | 64% helix, 9% strand | P62805 |
| H | Histone H2B type 1-J | protein | 95 | 72% helix, 4% strand | P06899 |
| I | DNA (185-mer) | dna | 172 | — | — |
| J | DNA (185-mer) | dna | 172 | — | — |
| K | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 218 | 11% helix, 27% strand | O96028 |
Ligands and binding sites
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 | 929 | 0.79 | 0.81 | 80 | empty |
| 2 | 965 | 0.74 | 0.78 | 64 | empty |
| 3 | 376 | 0.73 | 0.84 | 46 | empty |
| 4 | 840 | 0.71 | 0.77 | 73 | empty |
| 5 | 253 | 0.71 | 0.87 | 32 | empty |
Interfaces
38 interfaces between chains.
- I–J · 7809 Ų buried · 626 hydrogen bonds · nucleic-nucleic
- G–H · 2609 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2590 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2472 Ų buried · 19 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 P0C0S8
- Every structure of UniProt P06899
- Every structure of UniProt O96028
- Elsewhere: RCSB PDB 7E8D · PDBe 7E8D · UniProt P68431 · UniProt P62805 · UniProt P0C0S8 · UniProt P06899 · UniProt O96028
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