MolNFT v1 · #180806 · protein
Crystal structure of human survivin bound to histone H3T3PHK4AC peptide
7LBP · Baculoviral iap repeat-containing protein 5: “Crystal structure of human survivin bound to histone H3T3PHK4AC peptide”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.52). MolNFT v1 #180806 on GenesisL1: 3D…
- PDB
- 7LBP
- Type
- protein
- Length
- 287 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 5; Histone H3T3PHK4AC peptide
- UniProt
- O15392, P68431
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 53% 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, D | Histone H3T3PHK4AC peptide | protein | 6 | 0% helix, 33% strand | P68431 |
| C | Baculoviral iap repeat-containing protein 5 | protein | 138 | 56% helix, 7% strand | O15392 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
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 | 103 | 0.52 | 0.82 | 20 | empty |
| 2 | 120 | 0.52 | 0.81 | 22 | empty |
| 3 | 92 | 0.33 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 534 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 455 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 397 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation, phosphorylation).
Compared structures
- 7LBP · Crystal structure of human Survivin bound to histone H3T3phK4ac peptide · the same entry in another collection · chain D against D, 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
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain B against A, TM-score 0.69
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 7LBP · PDBe 7LBP · UniProt O15392 · UniProt P68431
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