Research workbench
Structural study on project id PH1539 from pyrococcus horikoshii OT3
Analyse Structural study on project id PH1539 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
- 2D3K
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase
- EC
- 3.1.1.29
- UniProt
- O74017
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 118 | 48% helix, 25% strand | O74017 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.42 | 0.76 | 21 | empty |
| 2 | 92 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1105 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2D3K · Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O74017 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (O74017) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O74017
- Elsewhere: RCSB PDB 2D3K · PDBe 2D3K · UniProt O74017
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