Research workbench
Crystal structure of survivin bound to the phosphorylated N- terminal tail of histone H3
Analyse Crystal structure of survivin bound to the phosphorylated N- terminal tail of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A0J
- Type
- protein
- Length
- 284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 5; Histone H3 peptide
- UniProt
- O15392
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 5 | protein | 136 | 54% helix, 7% strand | O15392 |
| B | Baculoviral iap repeat-containing protein 5 | protein | 137 | 52% helix, 7% strand | O15392 |
| C | Histone H3 peptide | protein | 6 | 0% helix, 33% strand | — |
| D | Histone H3 peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.61 | 0.84 | 27 | empty |
| 2 | 101 | 0.52 | 0.82 | 21 | empty |
| 3 | 92 | 0.47 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 485 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4A0J · Crystal structure of Survivin bound to the phosphorylated N-terminal tail of histone H3 · the same entry in another collection · chain A against A, TM-score 1.00
- O15392 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 5… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O15392
- Elsewhere: RCSB PDB 4A0J · PDBe 4A0J · UniProt O15392
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