Research workbench
Protein of unknown function from pyrococcus horikoshi
Analyse Protein of unknown function from pyrococcus horikoshi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DDZ
- Type
- protein
- Length
- 1,130 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 190AA long hypothetical protein
- Ligands
- GAI
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | 190AA long hypothetical protein | protein | 188 | 34% helix, 29% strand | — |
| E | 190AA long hypothetical protein | protein | 190 | 31% helix, 30% strand | — |
Ligands and binding sites
- GAI · Guanidine · ligand · 8 copies · chains A, C, E, B, D, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.89 | 0.90 | 104 | GAI |
| 2 | 249 | 0.71 | 0.86 | 42 | GOL |
| 3 | 312 | 0.71 | 0.84 | 46 | GOL |
| 4 | 288 | 0.69 | 0.83 | 39 | GOL |
| 5 | 282 | 0.68 | 0.83 | 37 | GOL |
Interfaces
14 interfaces between chains.
- A–B · 2184 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2144 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2115 Ų buried · 33 hydrogen bonds · protein-protein
- B–E · 764 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 661 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2DDZ · Protein of Unknown Function from Pyrococcus horikoshi · 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 2DDZ · PDBe 2DDZ
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