Research workbench
Crystal structure of yeast CDT1 (N terminal and middle domain), form 1.
Analyse Crystal structure of yeast CDT1 (N terminal and middle domain), form 1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ME9
- Type
- protein
- Length
- 1,129 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division cycle protein CDT1
- UniProt
- P47112
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division cycle protein CDT1 | protein | 380 | 39% helix, 19% strand | P47112 |
| B | Cell division cycle protein CDT1 | protein | 374 | 40% helix, 20% strand | P47112 |
| C | Cell division cycle protein CDT1 | protein | 375 | 41% helix, 21% strand | P47112 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.69 | 0.95 | 23 | GOL |
| 2 | 367 | 0.64 | 0.79 | 31 | empty |
| 3 | 199 | 0.61 | 0.82 | 37 | GOL |
| 4 | 155 | 0.60 | 0.83 | 32 | empty |
| 5 | 306 | 0.56 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 359 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 351 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 313 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5ME9 · Crystal structure of yeast Cdt1 (N terminal and middle domain), form 1. · the same entry in another collection · chain A against A, TM-score 1.00
- P47112 · AlphaFold monomer V2.0 prediction for cell division cycle protein CDT1 (P47112) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P47112
- Elsewhere: RCSB PDB 5ME9 · PDBe 5ME9 · UniProt P47112
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