Research workbench
Crystal structure of the CTF19-MCM21 kinetochore heterodimer from yeast
Analyse Crystal structure of the CTF19-MCM21 kinetochore heterodimer from yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZXU
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MCM21; CTF19
- UniProt
- Q6CVQ9, Q6CRN7
- Ligands
- CA
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MCM21 | protein | 211 | 29% helix, 33% strand | Q6CVQ9 |
| B | CTF19 | protein | 197 | 43% helix, 26% strand | Q6CRN7 |
| D | CTF19 | protein | 198 | 41% helix, 26% strand | Q6CRN7 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.61 | 0.89 | 17 | empty |
| 2 | 199 | 0.55 | 0.79 | 30 | empty |
| 3 | 97 | 0.44 | 0.79 | 23 | CA |
| 4 | 98 | 0.43 | 0.78 | 21 | CA |
| 5 | 121 | 0.42 | 0.76 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2835 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2820 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 290 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 243 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZXU · Crystal structure of the Ctf19-Mcm21 kinetochore heterodimer from yeast · the same entry in another collection · chain D against D, TM-score 1.00
- Q6CVQ9 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit MCM21 (Q6CVQ9) · a predicted model of the same protein · chain C against A, TM-score 0.88
- Q6CRN7 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit CTF19 (Q6CRN7) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 Q6CVQ9
- Every structure of UniProt Q6CRN7
- Elsewhere: RCSB PDB 3ZXU · PDBe 3ZXU · UniProt Q6CVQ9 · UniProt Q6CRN7
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