Research workbench
Crystal structure of human survivin bound to histone H3 T3PHK4ME1 peptide
Analyse Crystal structure of human survivin bound to histone H3 T3PHK4ME1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LBO
- 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 T3PHK4ME1 peptide
- UniProt
- O15392, P68431
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.50
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 | 137 | 53% helix, 7% strand | O15392 |
| B | Baculoviral iap repeat-containing protein 5 | protein | 136 | 53% helix, 7% strand | O15392 |
| C | Histone H3 T3PHK4ME1 peptide | protein | 5 | 0% helix, 40% strand | P68431 |
| F | Histone H3 T3PHK4ME1 peptide | protein | 6 | 0% helix, 33% strand | P68431 |
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
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.50 | 0.79 | 22 | empty |
| 2 | 104 | 0.48 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 582 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 424 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation, phosphorylation).
Compared structures
- 7LBO · Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.98
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain C against A, TM-score 0.80
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
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 7LBO · PDBe 7LBO · UniProt O15392 · UniProt P68431
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