Research workbench
Cryo-EM structure of the core centromere binding factor 3 complex
Analyse Cryo-EM structure of the core centromere binding factor 3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FE8
- Type
- protein
- Length
- 1,547 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centromere DNA-binding protein complex CBF3 subunit B; Suppressor of kinetochore protein…
- UniProt
- P40969, P52286, P35203
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Centromere DNA-binding protein complex CBF3 subunit B | protein | 524 | 67% helix, 2% strand | P40969 |
| B | Centromere DNA-binding protein complex CBF3 subunit B | protein | 512 | 68% helix, 1% strand | P40969 |
| C | Suppressor of kinetochore protein 1 | protein | 150 | 47% helix, 9% strand | P52286 |
| D | Centromere DNA-binding protein complex CBF3 subunit C | protein | 361 | 27% helix, 19% strand | P35203 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.83 | 0.85 | 89 | empty |
| 2 | 676 | 0.76 | 0.81 | 87 | empty |
| 3 | 350 | 0.75 | 0.86 | 59 | empty |
| 4 | 294 | 0.73 | 0.86 | 41 | empty |
| 5 | 73 | 0.73 | 0.96 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3037 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1843 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1429 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6FE8 · Cryo-EM structure of the core Centromere Binding Factor 3 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P40969 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P35203 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain D against A, TM-score 0.94
- P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 P40969
- Every structure of UniProt P52286
- Every structure of UniProt P35203
- Elsewhere: RCSB PDB 6FE8 · PDBe 6FE8 · UniProt P40969 · UniProt P52286 · UniProt P35203
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