MolNFT v1 · #15769 · protein
Crystal structure of SCSKP1-SCCDC4-cpd peptide complex
1NEX · Centromere DNA-binding protein complex CBF3 subunit D: “Crystal structure of SCSKP1-SCCDC4-cpd peptide complex”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1 #15769 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1NEX
- Type
- protein
- Length
- 1,159 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centromere DNA-binding protein complex CBF3 subunit D; CDC4 protein; GLL(TPO)PPQSG
- UniProt
- P52286, P07834
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Centromere DNA-binding protein complex CBF3 subunit D | protein | 129 | 54% helix, 10% strand | P52286 |
| B, D | CDC4 protein | protein | 444 | 16% helix, 44% strand | P07834 |
| C | Centromere DNA-binding protein complex CBF3 subunit D | protein | 130 | 54% helix, 10% strand | P52286 |
| E | GLL(TPO)PPQSG | protein | 4 | 0% helix, 0% strand | — |
| F | GLL(TPO)PPQSG | protein | 8 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.81 | 0.86 | 46 | empty |
| 2 | 1188 | 0.80 | 0.82 | 76 | empty |
| 3 | 413 | 0.70 | 0.81 | 33 | empty |
| 4 | 55 | 0.37 | 0.80 | 16 | empty |
| 5 | 101 | 0.36 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1389 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1359 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 451 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 337 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered, phosphorylation).
Compared structures
- 1NEX · Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex · the same entry in another collection · chain F against F, TM-score 1.00
- P07834 · AlphaFold monomer V2.0 prediction for cell division control protein 4 (P07834) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P52286
- Every structure of UniProt P07834
- Elsewhere: RCSB PDB 1NEX · PDBe 1NEX · UniProt P52286 · UniProt P07834
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.