MolNFT v1 · #150396 · protein
Core centromere binding factor 3 (CBF3) with monomeric NDC10
6GSA · Centromere DNA-binding protein complex CBF3 subunit B: “Core centromere binding factor 3 (CBF3) with monomeric NDC10”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #150396 on GenesisL1: 3D structure, binding…
- PDB
- 6GSA
- Type
- protein
- Length
- 1,999 residues
- Chains
- 5
- 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, P32504
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 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 |
| E | Centromere DNA-binding protein complex CBF3 subunit a | protein | 452 | 55% helix, 6% strand | P32504 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.86 | 0.87 | 116 | empty |
| 2 | 542 | 0.78 | 0.84 | 81 | empty |
| 3 | 337 | 0.76 | 0.87 | 53 | empty |
| 4 | 279 | 0.73 | 0.87 | 40 | empty |
| 5 | 401 | 0.71 | 0.82 | 58 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3042 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1429 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6GSA · Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 · the same entry in another collection · chain D against D, TM-score 1.00
- 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 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
- Every structure of UniProt P32504
- Elsewhere: RCSB PDB 6GSA · PDBe 6GSA · UniProt P40969 · UniProt P52286 · UniProt P35203 · UniProt P32504
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