MolNFT v1 · #78311 · protein
Crystal structure of ced-3 protease suppressor-6 (cps-6) from caenorhabditis elegans
3S5B · Endonuclease G: “Crystal structure of ced-3 protease suppressor-6 (cps-6) from caenorhabditis elegans”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.70). MolNFT v1 #78311 on GenesisL1: 3D structure, binding sites…
- PDB
- 3S5B
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease G
- EC
- 3.1.30.-
- UniProt
- Q95NM6
- Ligands
- MG
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease G (EC 3.1.30.-) | protein | 236 | 26% helix, 32% strand | Q95NM6 |
| B | Endonuclease G (EC 3.1.30.-) | protein | 243 | 27% helix, 31% strand | Q95NM6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.70 | 0.88 | 39 | empty |
| 2 | 61 | 0.44 | 0.82 | 17 | empty |
| 3 | 59 | 0.43 | 0.82 | 13 | empty |
| 4 | 93 | 0.38 | 0.76 | 18 | MG |
| 5 | 94 | 0.34 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1500 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3S5B · Crystal Structure of CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans · the same entry in another collection · chain A against A, TM-score 1.00
- Q95NM6 · AlphaFold monomer V2.0 prediction for endonuclease G, mitochondrial (Q95NM6) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q95NM6
- Elsewhere: RCSB PDB 3S5B · PDBe 3S5B · UniProt Q95NM6
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