Research workbench
Structure of PAG5_736 from P. aerophilum with three disulphide bonds
Analyse Structure of PAG5_736 from P. aerophilum with three disulphide bonds in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RKI
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q8ZYK2
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 101 | 24% helix, 41% strand | Q8ZYK2 |
| B | Hypothetical protein | protein | 97 | 31% helix, 37% strand | Q8ZYK2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · chains B
- P6G · Hexaethylene glycol · additive · chains B
- PG4 · Tetraethylene glycol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.56 | 0.78 | 29 | empty |
| 2 | 197 | 0.50 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1RKI · Structure of pag5_736 from P. aerophilum with three disulphide bonds · 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 Q8ZYK2
- Elsewhere: RCSB PDB 1RKI · PDBe 1RKI · UniProt Q8ZYK2
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