MolNFT v1 · #148214 · protein
CBF3 core complex
6F07 · Centromere DNA-binding protein complex CBF3 subunit B: “CBF3 core complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.82). MolNFT v1 #148214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F07
- Type
- protein
- Length
- 1,227 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centromere DNA-binding protein complex CBF3 subunit B; Suppressor of kinetochore protein 1
- UniProt
- P40969, P52286
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Centromere DNA-binding protein complex CBF3 subunit B | protein | 510 | 68% helix, 1% strand | P40969 |
| B | Centromere DNA-binding protein complex CBF3 subunit B | protein | 575 | 63% helix, 0% strand | P40969 |
| D | Suppressor of kinetochore protein 1 | protein | 142 | 51% helix, 8% strand | P52286 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.82 | 0.87 | 71 | empty |
| 2 | 817 | 0.79 | 0.82 | 88 | empty |
| 3 | 497 | 0.77 | 0.85 | 68 | empty |
| 4 | 90 | 0.69 | 0.93 | 24 | empty |
| 5 | 459 | 0.67 | 0.79 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2999 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1005 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6F07 · CBF3 Core Complex · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- 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 0.85
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
- Elsewhere: RCSB PDB 6F07 · PDBe 6F07 · UniProt P40969 · UniProt P52286
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