Research workbench
Cryo-EM structure of the CBF3-core-NDC10-dbd complex of the budding yeast kinetochore
Analyse Cryo-EM structure of the CBF3-core-NDC10-dbd complex of the budding yeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYP
- Type
- protein
- Length
- 2,147 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centromere DNA-binding protein complex CBF3 subunit B; Centromere DNA-binding protein…
- UniProt
- P40969, P35203, P52286, P32504
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 52% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Centromere DNA-binding protein complex CBF3 subunit B | protein | 534 | 63% helix, 2% strand | P40969 |
| A | Centromere DNA-binding protein complex CBF3 subunit C | protein | 423 | 30% helix, 11% strand | P35203 |
| C | Centromere DNA-binding protein complex CBF3 subunit B | protein | 527 | 66% helix, 1% strand | P40969 |
| D | Suppressor of kinetochore protein 1 | protein | 151 | 48% helix, 9% strand | P52286 |
| E | Centromere DNA-binding protein complex CBF3 subunit a | protein | 512 | 45% helix, 4% strand | P32504 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.83 | 0.85 | 114 | empty |
| 2 | 289 | 0.76 | 0.88 | 52 | empty |
| 3 | 866 | 0.75 | 0.79 | 67 | empty |
| 4 | 639 | 0.71 | 0.78 | 74 | empty |
| 5 | 413 | 0.70 | 0.82 | 60 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3381 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2502 Ų buried · 21 hydrogen bonds · protein-protein
- B–A · 1518 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1478 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 910 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GYP · Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore · the same entry in another collection · chain E against E, 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 C against A, TM-score 0.99
- P32504 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain E against A, TM-score 0.95
- P35203 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain A against A, TM-score 0.95
- P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain D 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 P35203
- Every structure of UniProt P52286
- Every structure of UniProt P32504
- Elsewhere: RCSB PDB 6GYP · PDBe 6GYP · UniProt P40969 · UniProt P35203 · UniProt P52286 · UniProt P32504
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