Research workbench
Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii OT3 at 2.20A resolution.
Analyse Crystal structure of a trimeric exonuclease phoexo I from pyrococcus horikoshii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YOU
- Type
- protein
- Length
- 630 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
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-5 exonuclease phoexo I | protein | 220 | 35% helix, 34% strand | A0A060P168 |
| B | 3-5 exonuclease phoexo I | protein | 199 | 30% helix, 39% strand | A0A060P168 |
| C | 3-5 exonuclease phoexo I | protein | 211 | 30% helix, 34% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.57 | 0.76 | 32 | MG |
| 2 | 291 | 0.54 | 0.75 | 38 | MG |
| 3 | 94 | 0.38 | 0.76 | 17 | empty |
| 4 | 72 | 0.31 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 855 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4YOU · 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 4YOU · PDBe 4YOU · UniProt A0A060P168
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