Research workbench
Crystal structure of project PH0463 from pyrococcus horikoshii OT3
Analyse Crystal structure of project PH0463 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
- 1WU8
- Type
- protein
- Length
- 768 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH0463
- UniProt
- O58212
- Ligands
- ADN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hypothetical protein PH0463 | protein | 256 | 26% helix, 32% strand | O58212 |
Ligands and binding sites
- ADN · Adenosine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.82 | 0.89 | 49 | empty |
| 2 | 104 | 0.79 | 0.98 | 22 | ADN |
| 3 | 104 | 0.78 | 0.98 | 24 | ADN |
| 4 | 103 | 0.78 | 0.98 | 26 | ADN |
| 5 | 97 | 0.34 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1436 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1433 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1429 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1WU8 · Crystal structure of project PH0463 from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O58212 · AlphaFold monomer V2.0 prediction for S-adenosyl-L-methionine hydrolase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O58212
- Elsewhere: RCSB PDB 1WU8 · PDBe 1WU8 · UniProt O58212
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