Research workbench
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp ncp (1:1 binding mode)
Analyse NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp ncp (1:1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CRP
- Type
- protein + DNA
- Length
- 1,338 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.-
- UniProt
- Q92133, P62799, Q6AZJ8, Q6AZK7, Q9BZ95
- Ligands
- SAM, ZN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 11 distinct chains · 43% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Histone H3 | protein | 103 | 56% helix, 5% strand | Q92133 |
| B | Histone H4 | protein | 82 | 56% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 109 | 38% helix, 4% strand | Q6AZJ8 |
| D | Histone H2B | protein | 95 | 68% helix, 2% strand | Q6AZK7 |
| E | Histone H3 | protein | 98 | 52% helix, 4% strand | Q92133 |
| F | Histone H4 | protein | 86 | 52% helix, 7% strand | P62799 |
| G | Histone H2A | protein | 110 | 45% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B | protein | 97 | 60% helix, 4% strand | Q6AZK7 |
| A | DNA (168-mer) | dna | 168 | — | — |
| K | DNA (168-mer) | dna | 168 | — | — |
| I | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.-) | protein | 222 | 9% helix, 18% strand | Q9BZ95 |
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 | 692 | 0.75 | 0.81 | 69 | empty |
| 2 | 756 | 0.74 | 0.79 | 53 | empty |
| 3 | 385 | 0.72 | 0.84 | 35 | empty |
| 4 | 308 | 0.71 | 0.85 | 33 | empty |
| 5 | 662 | 0.71 | 0.78 | 56 | empty |
Interfaces
39 interfaces between chains.
- A–K · 7769 Ų buried · 461 hydrogen bonds · nucleic-nucleic
- G–H · 2638 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 2622 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2604 Ų buried · 11 hydrogen bonds · protein-protein
- M–B · 2597 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (nonstandard).
Compared structures
- 7CRP · NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) · the same entry in another collection · chain I against I, TM-score 1.00
- P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9BZ95
- Elsewhere: RCSB PDB 7CRP · PDBe 7CRP · UniProt Q92133 · UniProt P62799 · UniProt Q6AZJ8 · UniProt Q6AZK7 · UniProt Q9BZ95
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