MolNFT v1 · #92643 · protein
Crystal structure of the SPC24-SPC25/CNN1 binding interface
4GEQ · Kinetochore protein SPC25: “Crystal structure of the SPC24-SPC25/CNN1 binding interface”. X-ray diffraction, 2 pockets (best druggability 0.71). MolNFT v1 #92643 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GEQ
- Type
- protein
- Length
- 331 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinetochore protein SPC25; Kinetochore protein SPC24; Kinetochore-associated protein CNN1
- UniProt
- P40014, Q04477, P43618
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinetochore protein SPC25 | protein | 89 | 44% helix, 25% strand | P40014 |
| B | Kinetochore protein SPC24 | protein | 58 | 41% helix, 24% strand | Q04477 |
| C | Kinetochore protein SPC25 | protein | 90 | 43% helix, 24% strand | P40014 |
| D | Kinetochore protein SPC24 | protein | 57 | 44% helix, 25% strand | Q04477 |
| E | Kinetochore-associated protein CNN1 | protein | 18 | 89% helix, 0% strand | P43618 |
| F | Kinetochore-associated protein CNN1 | protein | 19 | 84% helix, 0% strand | P43618 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.71 | 0.76 | 74 | empty |
| 2 | 55 | 0.30 | 0.76 | 15 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1133 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1100 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 639 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 586 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 251 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GEQ · Crystal structure of the Spc24-Spc25/Cnn1 binding interface · the same entry in another collection · chain F against F, TM-score 1.00
- P40014 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC25 (P40014) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q04477 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC24 (Q04477) · a predicted model of the same protein · chain D against A, TM-score 0.89
- P43618 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit CNN1 (P43618) · a predicted model of the same protein · chain E against A, TM-score 0.76
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 P40014
- Every structure of UniProt Q04477
- Every structure of UniProt P43618
- Elsewhere: RCSB PDB 4GEQ · PDBe 4GEQ · UniProt P40014 · UniProt Q04477 · UniProt P43618
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