Research workbench
Structure of chromosomal passenger complex (cpc) bound to phosphorylated histone 3 peptide at 1.8 a.
Analyse Structure of chromosomal passenger complex (cpc) bound to phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YIF
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 5; Borealin; Inner centromere protein…
- UniProt
- O15392, Q53HL2, Q9NQS7
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 5 | protein | 130 | 51% helix, 8% strand | O15392 |
| B | Borealin | protein | 56 | 86% helix, 2% strand | Q53HL2 |
| C | Inner centromere protein | protein | 37 | 84% helix, 0% strand | Q9NQS7 |
| D | Phosphorylated (THR3) histone H3 | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
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 | 72 | 0.34 | 0.76 | 13 | empty |
| 2 | 57 | 0.25 | 0.72 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1303 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6YIF · Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3… · 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 A against A, TM-score 0.96
- Q53HL2 · AlphaFold monomer V2.0 prediction for borealin (Q53HL2) · a predicted model of the same protein · chain B against A, TM-score 0.90
- Q9NQS7 · AlphaFold monomer V2.0 prediction for inner centromere protein (Q9NQS7) · a predicted model of the same protein · chain C against A, TM-score 0.71
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 Q53HL2
- Every structure of UniProt Q9NQS7
- Elsewhere: RCSB PDB 6YIF · PDBe 6YIF · UniProt O15392 · UniProt Q53HL2 · UniProt Q9NQS7
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