Research workbench
Crystal structure of the WHSC1 PWWP1 domain
Analyse Crystal structure of the WHSC1 PWWP1 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VC8
- Type
- protein + DNA
- Length
- 288 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD2; Dodeca-2-deoxy-nucleotide, poorly resolved by…
- EC
- 2.1.1.43
- UniProt
- O96028
- Ligands
- DN, UNX
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 125 | 41% helix, 22% strand | O96028 |
| B | Histone-lysine N-methyltransferase NSD2 (EC 2.1.1.43) | protein | 125 | 38% helix, 22% strand | O96028 |
| W, X, Y | Dodeca-2-deoxy-nucleotide, poorly resolved by electron density | dna | 12 | — | — |
| Z | DNA (5'-D(P*CP*TP*(DN))-3') | dna | 2 | — | — |
Ligands and binding sites
- DN · Unknown 2'-deoxynucleotide · ligand · chains Z
- UNX · Unknown atom or ion · ion · 39 copies · chains A, B, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.78 | 0.81 | 87 | UNX |
Interfaces
10 interfaces between chains.
- A–B · 1017 Ų buried · 26 hydrogen bonds · protein-protein
- W–X · 520 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- W–Z · 173 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- W–Y · 136 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–W · 123 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified, 1 covalent (engineered, 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 O96028
- Elsewhere: RCSB PDB 5VC8 · PDBe 5VC8 · UniProt O96028
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