MolNFT v1 · #126816 · protein
Crystal structure of yeast CDT1 (N terminal and middle domain), form 1.
5ME9 · Cell division cycle protein CDT1: “Crystal structure of yeast CDT1 (N terminal and middle domain), form 1.”. X-ray diffraction, 1 ligand (SO4), 18 pockets (best druggability 0.69). MolNFT v1 #126816 on GenesisL1: 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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