Research workbench
Structure of yeast SSD1, a pseudonuclease
Analyse Structure of yeast SSD1, a pseudonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AM1
- Type
- protein
- Length
- 1,621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein SSD1
- UniProt
- P24276
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein SSD1 | protein | 810 | 33% helix, 24% strand | P24276 |
| B | Protein SSD1 | protein | 811 | 33% helix, 24% strand | P24276 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.86 | 0.88 | 90 | 1PE |
| 2 | 1126 | 0.85 | 0.86 | 95 | empty |
| 3 | 1104 | 0.80 | 0.82 | 108 | empty |
| 4 | 51 | 0.69 | 0.97 | 22 | empty |
| 5 | 159 | 0.63 | 0.85 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P24276
- Elsewhere: RCSB PDB 7AM1 · PDBe 7AM1 · UniProt P24276
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