Research workbench
Crystal structure of a DUF89 family protein (PH1575) from pyrococcus horikoshii at 2.04 a resolution
Analyse Crystal structure of a DUF89 family protein (PH1575) 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
- 2G8L
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 287AA long hypothetical protein
- Ligands
- UNL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 287AA long hypothetical protein | protein | 285 | 54% helix, 13% strand | — |
| B | 287AA long hypothetical protein | protein | 286 | 54% helix, 13% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.74 | 0.84 | 47 | UNL |
| 2 | 446 | 0.70 | 0.81 | 42 | UNL |
| 3 | 96 | 0.37 | 0.75 | 21 | empty |
| 4 | 53 | 0.28 | 0.75 | 16 | empty |
| 5 | 58 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1180 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2G8L · Crystal structure of a duf89 family protein (ph1575) from pyrococcus horikoshii at 2.04 A… · 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
- Elsewhere: RCSB PDB 2G8L · PDBe 2G8L
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