MolNFT v1 · #151898 · protein
Structure of the YSH1-MPE1 nuclease complex from S.CEREVISIAE
6I1D · Endoribonuclease YSH1: “Structure of the YSH1-MPE1 nuclease complex from S.CEREVISIAE”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.78). MolNFT v1 #151898 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6I1D
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease YSH1; Protein MPE1
- EC
- 3.1.27.-
- UniProt
- Q06224, P35728
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease YSH1 (EC 3.1.27.-) | protein | 458 | 31% helix, 22% strand | Q06224 |
| B | Protein MPE1 | protein | 88 | 16% helix, 39% strand | P35728 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.78 | 0.86 | 69 | empty |
| 2 | 54 | 0.61 | 0.93 | 22 | empty |
| 3 | 96 | 0.38 | 0.76 | 17 | empty |
| 4 | 90 | 0.37 | 0.76 | 17 | empty |
| 5 | 108 | 0.36 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6I1D · Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P35728 · AlphaFold monomer V2.0 prediction for protein MPE1 (P35728) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q06224 · AlphaFold monomer V2.0 prediction for endoribonuclease YSH1 (Q06224) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q06224
- Every structure of UniProt P35728
- Elsewhere: RCSB PDB 6I1D · PDBe 6I1D · UniProt Q06224 · UniProt P35728
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