Research workbench
Structure of protein of unknown function PH0006 from pyrococcus horikoshii
Analyse Structure of protein of unknown function PH0006 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
- 2GFQ
- Type
- protein
- Length
- 846 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0204 protein PH0006
- UniProt
- O57774
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0204 protein PH0006 | protein | 288 | 35% helix, 28% strand | O57774 |
| B | UPF0204 protein PH0006 | protein | 280 | 34% helix, 29% strand | O57774 |
| C | UPF0204 protein PH0006 | protein | 278 | 34% helix, 29% strand | O57774 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.60 | 0.78 | 51 | empty |
| 2 | 207 | 0.57 | 0.80 | 31 | empty |
| 3 | 203 | 0.49 | 0.76 | 29 | empty |
| 4 | 166 | 0.47 | 0.76 | 28 | empty |
| 5 | 119 | 0.36 | 0.73 | 20 | SO4 |
Interfaces
2 interfaces between chains.
- B–C · 714 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 2GFQ · Structure of Protein of Unknown Function PH0006 from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O57774 · AlphaFold monomer V2.0 prediction for D-aminoacyl-tRNA deacylase (O57774) · a predicted model of the same protein · chain C 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 O57774
- Elsewhere: RCSB PDB 2GFQ · PDBe 2GFQ · UniProt O57774
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