MolNFT v1 · #115979 · protein
Structure of S. cerevisiae HRR25:MAM1 complex, form 2
5CZO · Casein kinase I homolog HRR25: “Structure of S. cerevisiae HRR25:MAM1 complex, form 2”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.70). MolNFT v1 #115979 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5CZO
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase I homolog HRR25; Monopolin complex subunit MAM1
- EC
- 2.7.11.1
- UniProt
- P29295, P40065
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase I homolog HRR25 (EC 2.7.11.1) | protein | 374 | 44% helix, 15% strand | P29295 |
| C, D | Monopolin complex subunit MAM1 | protein | 101 | 47% helix, 2% strand | P40065 |
| B | Casein kinase I homolog HRR25 (EC 2.7.11.1) | protein | 374 | 43% helix, 16% strand | P29295 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.70 | 0.84 | 34 | empty |
| 2 | 287 | 0.68 | 0.83 | 37 | empty |
| 3 | 282 | 0.63 | 0.80 | 37 | empty |
| 4 | 244 | 0.63 | 0.81 | 35 | empty |
| 5 | 215 | 0.50 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2900 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2821 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 modified (methylation).
Compared structures
- 5CZO · Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 · the same entry in another collection · chain A against A, TM-score 1.00
- P29295 · AlphaFold monomer V2.0 prediction for casein kinase I homolog HRR25 (P29295) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P40065 · AlphaFold monomer V2.0 prediction for monopolin complex subunit MAM1 (P40065) · a predicted model of the same protein · chain C 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 P29295
- Every structure of UniProt P40065
- Elsewhere: RCSB PDB 5CZO · PDBe 5CZO · UniProt P29295 · UniProt P40065
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