Research workbench
Crystal structure of the PH0671 protein from pyrococcus horikoshii OT3
Analyse Crystal structure of the PH0671 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
- 1WY1
- Type
- protein
- Length
- 423 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH0671
- EC
- 2.5.1.-
- UniProt
- O58404
- Ligands
- MG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein PH0671 (EC 2.5.1.-) | protein | 142 | 77% helix, 0% strand | O58404 |
| B | Hypothetical protein PH0671 (EC 2.5.1.-) | protein | 143 | 78% helix, 0% strand | O58404 |
| C | Hypothetical protein PH0671 (EC 2.5.1.-) | protein | 138 | 76% helix, 0% strand | O58404 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.60 | 0.80 | 31 | empty |
| 2 | 217 | 0.52 | 0.77 | 30 | empty |
| 3 | 223 | 0.51 | 0.76 | 31 | empty |
| 4 | 198 | 0.48 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 761 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 742 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 734 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1WY1 · Crystal Structure of the PH0671 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 O58404
- Elsewhere: RCSB PDB 1WY1 · PDBe 1WY1 · UniProt O58404
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