Research workbench
Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3 in complex with phosphate ion
Analyse Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E5F
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH0510
- UniProt
- O58246
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein PH0510 | protein | 325 | 46% helix, 17% strand | O58246 |
| B | Hypothetical protein PH0510 | protein | 324 | 46% helix, 17% strand | O58246 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.88 | 0.93 | 56 | EDO |
| 2 | 117 | 0.78 | 0.97 | 26 | PO4 |
| 3 | 114 | 0.77 | 0.97 | 26 | PO4 |
| 4 | 161 | 0.63 | 0.85 | 23 | empty |
| 5 | 141 | 0.63 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2772 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 2E5F · Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3 in complex with… · 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 O58246
- Elsewhere: RCSB PDB 2E5F · PDBe 2E5F · UniProt O58246
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