MolNFT v1 · #62013 · protein
Crystal structure of an uncharacterized amidohydrolase from saccharomyces cerevisiae
3E2V · 3'-5'-exonuclease: “Crystal structure of an uncharacterized amidohydrolase from saccharomyces cerevisiae”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.72). MolNFT v1 #62013 on GenesisL1: 3D structure, binding…
- PDB
- 3E2V
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3'-5'-exonuclease
- UniProt
- A6ZKP4
- Ligands
- MG
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3'-5'-exonuclease | protein | 363 | 47% helix, 16% strand | A6ZKP4 |
| B | 3'-5'-exonuclease | protein | 362 | 47% helix, 16% strand | A6ZKP4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.72 | 0.80 | 48 | empty |
| 2 | 209 | 0.52 | 0.77 | 25 | MG |
| 3 | 218 | 0.52 | 0.77 | 27 | MG |
| 4 | 56 | 0.45 | 0.84 | 17 | GOL |
| 5 | 55 | 0.45 | 0.84 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3E2V · Crystal structure of an uncharacterized amidohydrolase from Saccharomyces cerevisiae · the same entry in another collection · 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 A6ZKP4
- Elsewhere: RCSB PDB 3E2V · PDBe 3E2V · UniProt A6ZKP4
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