Research workbench
Crystal structure of an extended dwarf NDC80 complex
Analyse Crystal structure of an extended dwarf NDC80 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TD8
- Type
- protein
- Length
- 786 residues
- Chains
- 5
- 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
- HG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinetochore protein NDC80 | protein | 256 | 75% helix, 0% strand | P40460 |
| B | Kinetochore protein NUF2 | protein | 186 | 72% helix, 0% strand | P33895 |
| C | Kinetochore protein SPC24 | protein | 111 | 54% helix, 11% strand | Q04477 |
| D | Kinetochore protein SPC25 | protein | 128 | 60% helix, 13% strand | P40014 |
| E | Nanobody | protein | 105 | 3% helix, 53% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 6 copies · chains A, B, D
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 | 83 | 0.73 | 0.96 | 20 | empty |
| 2 | 370 | 0.72 | 0.83 | 36 | empty |
| 3 | 321 | 0.68 | 0.82 | 30 | empty |
| 4 | 322 | 0.65 | 0.80 | 41 | HG |
| 5 | 221 | 0.58 | 0.80 | 30 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2968 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1490 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 941 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 872 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5TD8 · Crystal structure of an Extended Dwarf Ndc80 Complex · the same entry in another collection · chain E against E, TM-score 1.00
- P40014 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC25 (P40014) · a predicted model of the same protein · chain D against A, TM-score 0.76
- P33895 · AlphaFold monomer V2.0 prediction for kinetochore protein NUF2 (P33895) · a predicted model of the same protein · chain B against A, TM-score 0.74
- P40460 · AlphaFold monomer V2.0 prediction for kinetochore protein NDC80 (P40460) · a predicted model of the same protein · chain A against A, TM-score 0.68
- Q04477 · AlphaFold monomer V2.0 prediction for kinetochore protein SPC24 (Q04477) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 5TD8 · PDBe 5TD8 · UniProt P40460 · UniProt P33895 · UniProt Q04477 · UniProt P40014
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