MolNFT v1 · #175469 · protein + DNA
NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp ncp
7CRO · Histone H3: “NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp ncp”. Electron microscopy, 2 ligands (SAM, ZN), 20 pockets (best druggability 0.74). MolNFT v1 #175469 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7CRO
- Type
- protein + DNA
- Length
- 1,335 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (168-mer); Histone-lysine…
- EC
- 2.1.1.357
- UniProt
- Q92133, P62799, Q6AZJ8, Q6AZK7, O96028
- Ligands
- SAM, ZN
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 11 distinct chains · 42% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Histone H3 | protein | 103 | 49% helix, 4% strand | Q92133 |
| B | Histone H4 | protein | 82 | 57% helix, 6% strand | P62799 |
| C | Histone H2A | protein | 109 | 45% helix, 6% strand | Q6AZJ8 |
| D | Histone H2B | protein | 95 | 65% helix, 4% strand | Q6AZK7 |
| E | Histone H3 | protein | 98 | 47% helix, 4% strand | Q92133 |
| F | Histone H4 | protein | 86 | 50% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 110 | 45% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B | protein | 97 | 57% helix, 4% strand | Q6AZK7 |
| A | DNA (168-mer) | dna | 168 | — | — |
| K | DNA (168-mer) | dna | 168 | — | — |
| I | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.357) | protein | 219 | 6% helix, 16% 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 | 624 | 0.74 | 0.81 | 54 | empty |
| 2 | 391 | 0.74 | 0.85 | 33 | empty |
| 3 | 573 | 0.73 | 0.81 | 63 | empty |
| 4 | 405 | 0.72 | 0.84 | 38 | empty |
| 5 | 529 | 0.71 | 0.80 | 52 | empty |
Interfaces
37 interfaces between chains.
- A–K · 7626 Ų buried · 486 hydrogen bonds · nucleic-nucleic
- G–H · 2664 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 2664 Ų buried · 9 hydrogen bonds · protein-protein
- M–B · 2620 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2608 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard).
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 Q92133
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt Q6AZK7
- Every structure of UniProt O96028
- Elsewhere: RCSB PDB 7CRO · PDBe 7CRO · UniProt Q92133 · UniProt P62799 · UniProt Q6AZJ8 · UniProt Q6AZK7 · UniProt O96028
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