MolNFT v1 · #140055 · protein
The crystal structure of CSM2-PSY3-SHU1-SHU2 complex from budding yeast
5XYN · Platinum sensitivity protein 3: “The crystal structure of CSM2-PSY3-SHU1-SHU2 complex from budding yeast”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.66). MolNFT v1 #140055 on GenesisL1: 3D structure, binding…
- PDB
- 5XYN
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platinum sensitivity protein 3; Chromosome segregation in meiosis protein 2; Suppressor…
- UniProt
- Q12318, P40465, P38751, P38957
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platinum sensitivity protein 3 | protein | 210 | 40% helix, 21% strand | Q12318 |
| B | Chromosome segregation in meiosis protein 2 | protein | 186 | 51% helix, 20% strand | P40465 |
| C | Suppressor of hu sensitivity involved in recombination protein 1 | protein | 146 | 49% helix, 17% strand | P38751 |
| D | Suppressor of hydroxyurea sensitivity protein 2 | protein | 205 | 39% helix, 15% strand | P38957 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.66 | 0.78 | 55 | empty |
| 2 | 122 | 0.45 | 0.77 | 22 | empty |
| 3 | 57 | 0.36 | 0.78 | 13 | empty |
| 4 | 87 | 0.36 | 0.75 | 23 | empty |
| 5 | 90 | 0.34 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1573 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1531 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XYN · The crystal structure of Csm2-Psy3-Shu1-Shu2 complex from budding yeast · the same entry in another collection · chain D against D, TM-score 1.00
- P40465 · AlphaFold monomer V2.0 prediction for chromosome segregation in meiosis protein 2 (P40465) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P38957 · AlphaFold monomer V2.0 prediction for suppressor of hydroxyurea sensitivity protein 2… · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q12318 · AlphaFold monomer V2.0 prediction for platinum sensitivity protein 3 (Q12318) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P38751 · AlphaFold monomer V2.0 prediction for suppressor of hu sensitivity involved in… · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q12318
- Every structure of UniProt P40465
- Every structure of UniProt P38751
- Every structure of UniProt P38957
- Elsewhere: RCSB PDB 5XYN · PDBe 5XYN · UniProt Q12318 · UniProt P40465 · UniProt P38751 · UniProt P38957
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