MolNFT v1 · #177184 · protein + DNA
Human SETD2 bound to a nucleosome containing oncohistone mutations
7EA8 · Histone-lysine N-methyltransferase SETD2: “Human SETD2 bound to a nucleosome containing oncohistone mutations”. Electron microscopy, 2 ligands (SAM, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #177184 on GenesisL1: 3D…
- PDB
- 7EA8
- Type
- protein + DNA
- Length
- 1,228 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD2; Histone H3.3; Histone H4; Histone H2A type 1-D…
- EC
- 2.1.1.359, 2.1.1.-
- UniProt
- Q9BYW2, P20671, Q16778
- Ligands
- SAM, ZN
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 10 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.359, 2.1.1.-) | protein | 245 | 10% helix, 17% strand | Q9BYW2 |
| A | Histone H3.3 | protein | 101 | 61% helix, 5% strand | — |
| B, F | Histone H4 | protein | 78 | 65% helix, 9% strand | — |
| C | Histone H2A type 1-D | protein | 104 | 52% helix, 6% strand | P20671 |
| D | Histone H2B type 2-E | protein | 92 | 74% helix, 4% strand | Q16778 |
| E | Histone H3.3 | protein | 94 | 66% helix, 3% strand | — |
| G | Histone H2A type 1-D | protein | 103 | 50% helix, 7% strand | P20671 |
| H | Histone H2B type 2-E | protein | 89 | 78% helix, 4% strand | Q16778 |
| I | 601-DNA | dna | 122 | — | — |
| J | 601-DNA | dna | 122 | — | — |
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 | 1097 | 0.79 | 0.81 | 79 | empty |
| 2 | 1082 | 0.78 | 0.80 | 102 | empty |
| 3 | 531 | 0.77 | 0.84 | 52 | SAM |
| 4 | 527 | 0.73 | 0.82 | 57 | empty |
| 5 | 614 | 0.71 | 0.79 | 57 | empty |
Interfaces
38 interfaces between chains.
- I–J · 5627 Ų buried · 412 hydrogen bonds · nucleic-nucleic
- G–H · 2555 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2532 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 2488 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2486 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 Q9BYW2
- Every structure of UniProt P20671
- Every structure of UniProt Q16778
- Elsewhere: RCSB PDB 7EA8 · PDBe 7EA8 · UniProt Q9BYW2 · UniProt P20671 · UniProt Q16778
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