Research workbench
Crystal structure of human survivin bound to histone H3 (C2 space group).
Analyse Crystal structure of human survivin bound to histone H3 (C2 space group). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UEF
- Type
- protein
- Length
- 282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 5; N-terminal fragment of histone H3
- UniProt
- O15392
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 5 | protein | 136 | 55% helix, 7% strand | O15392 |
| C | Baculoviral iap repeat-containing protein 5 | protein | 137 | 55% helix, 7% strand | O15392 |
| B | N-terminal fragment of histone H3 | protein | 5 | 0% helix, 40% strand | — |
| D | N-terminal fragment of histone H3 | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.53 | 0.82 | 20 | empty |
| 2 | 136 | 0.50 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 567 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 304 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3UEF · Crystal structure of human Survivin bound to histone H3 (C2 space group). · 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 C 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 3UEF · PDBe 3UEF · UniProt O15392
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