Research workbench
Structure of a borealin-incenp-survivin complex
Analyse Structure of a borealin-incenp-survivin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YIE
- Type
- protein
- Length
- 473 residues
- Chains
- 6
- 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
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 5 | protein | 135 | 50% helix, 7% strand | O15392 |
| B | Borealin | protein | 62 | 89% helix, 2% strand | Q53HL2 |
| C | Inner centromere protein | protein | 40 | 90% helix, 0% strand | Q9NQS7 |
| D | Baculoviral iap repeat-containing protein 5 | protein | 133 | 48% helix, 7% strand | O15392 |
| E | Borealin | protein | 60 | 88% helix, 2% strand | Q53HL2 |
| F | Inner centromere protein | protein | 43 | 81% helix, 0% strand | Q9NQS7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.70 | 0.96 | 16 | empty |
| 2 | 510 | 0.63 | 0.76 | 44 | empty |
| 3 | 112 | 0.45 | 0.78 | 24 | empty |
| 4 | 110 | 0.42 | 0.77 | 24 | empty |
| 5 | 73 | 0.32 | 0.74 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1466 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1380 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 901 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 853 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 706 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YIE · Structure of a Borealin-INCENP-Survivin complex · 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 0.95
- Q53HL2 · AlphaFold monomer V2.0 prediction for borealin (Q53HL2) · a predicted model of the same protein · chain B against A, TM-score 0.89
- Q9NQS7 · AlphaFold monomer V2.0 prediction for inner centromere protein (Q9NQS7) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 6YIE · PDBe 6YIE · UniProt O15392 · UniProt Q53HL2 · UniProt Q9NQS7
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