Research workbench
Crystal structure of PH1918 protein from pyrococcus horikoshii OT3
Analyse Crystal structure of PH1918 protein from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D16
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH1918
- UniProt
- O59581
- Ligands
- NA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hypothetical protein PH1918 | protein | 162 | 32% helix, 35% strand | O59581 |
| B, D | Hypothetical protein PH1918 | protein | 161 | 32% helix, 35% strand | O59581 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.57 | 0.75 | 32 | empty |
| 2 | 93 | 0.40 | 0.78 | 24 | empty |
| 3 | 83 | 0.40 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 894 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 890 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2D16 · Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3 · 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 O59581
- Elsewhere: RCSB PDB 2D16 · PDBe 2D16 · UniProt O59581
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