MolNFT v1 · #111368 · protein
Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 at 2.15A resolution
4YOT · 3-5 exonuclease phoexo I: “Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 at 2.15A resolution”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.41). MolNFT v1 #111368 on…
- PDB
- 4YOT
- Type
- protein
- Length
- 663 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-5 exonuclease phoexo I
- UniProt
- A0A060P168
- Ligands
- MG
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-5 exonuclease phoexo I | protein | 225 | 36% helix, 32% strand | A0A060P168 |
| B | 3-5 exonuclease phoexo I | protein | 220 | 33% helix, 36% strand | A0A060P168 |
| C | 3-5 exonuclease phoexo I | protein | 218 | 38% helix, 33% strand | A0A060P168 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.41 | 0.76 | 21 | MG |
| 2 | 129 | 0.41 | 0.75 | 20 | MG |
| 3 | 85 | 0.35 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 851 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 847 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4YOT · Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at… · 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 A0A060P168
- Elsewhere: RCSB PDB 4YOT · PDBe 4YOT · UniProt A0A060P168
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