Research workbench
Crystal structure of the human kinetochore MIS12-cenp-C complex
Analyse Crystal structure of the human kinetochore MIS12-cenp-C complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LSK
- Type
- protein
- Length
- 761 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein MIS12 homolog; Polyamine-modulated factor 1; Kinetochore-associated protein DSN1…
- UniProt
- Q9H081, Q6P1K2, Q9H410, Q96IY1, Q03188
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein MIS12 homolog | protein | 199 | 74% helix, 0% strand | Q9H081 |
| B | Polyamine-modulated factor 1 | protein | 173 | 81% helix, 0% strand | Q6P1K2 |
| D | Kinetochore-associated protein DSN1 homolog | protein | 178 | 76% helix, 0% strand | Q9H410 |
| N | Kinetochore-associated protein NSL1 homolog | protein | 173 | 66% helix, 2% strand | Q96IY1 |
| P | Centromere protein C | protein | 38 | 18% helix, 0% strand | Q03188 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.67 | 0.79 | 41 | empty |
| 2 | 197 | 0.56 | 0.80 | 25 | empty |
Interfaces
10 interfaces between chains.
- A–B · 4409 Ų buried · 17 hydrogen bonds · protein-protein
- D–N · 3785 Ų buried · 20 hydrogen bonds · protein-protein
- A–N · 2038 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1415 Ų buried · 7 hydrogen bonds · protein-protein
- A–P · 1292 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5LSK · Crystal structure of the human kinetochore MIS12-cenp-C complex · the same entry in another collection · chain P against P, TM-score 1.00
- Q6P1K2 · AlphaFold monomer V2.0 prediction for polyamine-modulated factor 1 (Q6P1K2) · a predicted model of the same protein · chain B against A, TM-score 0.91
- Q9H410 · AlphaFold monomer V2.0 prediction for kinetochore-associated protein DSN1 homolog (Q9H410) · a predicted model of the same protein · chain D against A, TM-score 0.62
- Q9H081 · AlphaFold monomer V2.0 prediction for protein MIS12 homolog (Q9H081) · a predicted model of the same protein · chain A against A, TM-score 0.50
- Q96IY1 · AlphaFold monomer V2.0 prediction for kinetochore-associated protein NSL1 homolog (Q96IY1) · a predicted model of the same protein · chain N against A, TM-score 0.45
- Q03188 · AlphaFold monomer V2.0 prediction for centromere protein C (Q03188) · a predicted model of the same protein · chain P against A, TM-score 0.33
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 Q9H081
- Every structure of UniProt Q6P1K2
- Every structure of UniProt Q9H410
- Every structure of UniProt Q96IY1
- Every structure of UniProt Q03188
- Elsewhere: RCSB PDB 5LSK · PDBe 5LSK · UniProt Q9H081 · UniProt Q6P1K2 · UniProt Q9H410 · UniProt Q96IY1 · UniProt Q03188
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