Research workbench
Crystal structure of a dwarf NDC80 tetramer
Analyse Crystal structure of a dwarf NDC80 tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TCS
- Type
- protein
- Length
- 688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinetochore protein NDC80; Kinetochore protein NUF2; Kinetochore protein SPC24…
- UniProt
- P40460, P33895, Q04477, P40014
- Ligands
- MG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinetochore protein NDC80 | protein | 266 | 75% helix, 0% strand | P40460 |
| B | Kinetochore protein NUF2 | protein | 211 | 66% helix, 0% strand | P33895 |
| C | Kinetochore protein SPC24 | protein | 97 | 54% helix, 12% strand | Q04477 |
| D | Kinetochore protein SPC25 | protein | 114 | 51% helix, 21% strand | P40014 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.97 | 16 | empty |
| 2 | 169 | 0.59 | 0.82 | 23 | empty |
| 3 | 67 | 0.59 | 0.89 | 20 | empty |
| 4 | 222 | 0.57 | 0.79 | 28 | empty |
| 5 | 148 | 0.52 | 0.80 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3314 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1264 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1067 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 858 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 790 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 5TCS · Crystal structure of a Dwarf Ndc80 Tetramer · the same entry in another collection · chain D against D, TM-score 1.00
- P40460 · AlphaFold monomer V2.0 prediction for kinetochore protein NDC80 (P40460) · a predicted model of the same protein · chain A against A, TM-score 0.85
- P40014 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC25 (P40014) · a predicted model of the same protein · chain D against A, TM-score 0.73
- P33895 · AlphaFold monomer V2.0 prediction for kinetochore protein NUF2 (P33895) · a predicted model of the same protein · chain B against A, TM-score 0.73
- Q04477 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC24 (Q04477) · a predicted model of the same protein · chain C against A, TM-score 0.57
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 P40460
- Every structure of UniProt P33895
- Every structure of UniProt Q04477
- Every structure of UniProt P40014
- Elsewhere: RCSB PDB 5TCS · PDBe 5TCS · UniProt P40460 · UniProt P33895 · UniProt Q04477 · UniProt P40014
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