Research workbench
Crystal structure of the human kinetochore MIS12-cenp-C delta-HEAD2 complex
Analyse Crystal structure of the human kinetochore MIS12-cenp-C delta-HEAD2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LSJ
- Type
- protein
- Length
- 1,177 residues
- Chains
- 10
- 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
- 15 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein MIS12 homolog | protein | 199 | 76% helix, 0% strand | Q9H081 |
| B, E | Polyamine-modulated factor 1 | protein | 173 | 81% helix, 0% strand | Q6P1K2 |
| D, F | Kinetochore-associated protein DSN1 homolog | protein | 101 | 84% helix, 0% strand | Q9H410 |
| N | Kinetochore-associated protein NSL1 homolog | protein | 101 | 74% helix, 0% strand | Q96IY1 |
| P | Centromere protein C | protein | 13 | 0% helix, 0% strand | Q03188 |
| G | Kinetochore-associated protein NSL1 homolog | protein | 102 | 75% helix, 0% strand | Q96IY1 |
| Q | Centromere protein C | protein | 15 | 0% helix, 0% strand | Q03188 |
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.75 | 0.78 | 92 | empty |
| 2 | 666 | 0.69 | 0.77 | 62 | empty |
| 3 | 143 | 0.55 | 0.82 | 20 | empty |
| 4 | 71 | 0.38 | 0.78 | 17 | empty |
| 5 | 101 | 0.38 | 0.75 | 18 | empty |
Interfaces
23 interfaces between chains.
- A–B · 4443 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 4375 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 2171 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 2065 Ų buried · 14 hydrogen bonds · protein-protein
- D–N · 2060 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5LSJ · CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX · the same entry in another collection · chain Q against Q, 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 0.86
- 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 0.65
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 5LSJ · PDBe 5LSJ · UniProt Q9H081 · UniProt Q6P1K2 · UniProt Q9H410 · UniProt Q96IY1 · UniProt Q03188
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