Research workbench
NDC10: a platform for inner kinetochore assembly in budding yeast
Analyse NDC10: a platform for inner kinetochore assembly in budding yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T79
- Type
- protein + DNA
- Length
- 835 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)- 3'); DNA…
- UniProt
- Q6CPM4
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)- 3') | dna | 15 | — | — |
| E | DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3') | dna | 14 | — | — |
| F | DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)- 3') | dna | 15 | — | — |
| A, D | KLLA0E03807P | protein | 388 | 52% helix, 6% strand | Q6CPM4 |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.74 | 0.98 | 16 | empty |
| 2 | 331 | 0.71 | 0.83 | 40 | empty |
| 3 | 318 | 0.71 | 0.84 | 36 | empty |
| 4 | 385 | 0.70 | 0.82 | 35 | empty |
| 5 | 560 | 0.67 | 0.78 | 62 | empty |
Interfaces
7 interfaces between chains.
- A–D · 886 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 637 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- E–F · 548 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- F–D · 409 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–A · 404 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3T79 · Ndc10: a platform for inner kinetochore assembly in budding yeast · the same entry in another collection · chain B against B, TM-score 1.00
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 Q6CPM4
- Elsewhere: RCSB PDB 3T79 · PDBe 3T79 · UniProt Q6CPM4
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