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Crystal structure of a pyrophosphatase (AF1178) from archaeoglobus fulgidus dsm 4304 at 1.80 a resolution
Analyse Crystal structure of a pyrophosphatase (AF1178) from archaeoglobus fulgidus dsm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QGP
- Type
- protein
- Length
- 215 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrophosphatase
- UniProt
- O29089
- Ligands
- MG, NA, CL
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrophosphatase | protein | 108 | 78% helix, 4% strand | O29089 |
| B | Pyrophosphatase | protein | 107 | 78% helix, 4% strand | O29089 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.46 | 0.78 | 18 | empty |
| 2 | 94 | 0.41 | 0.77 | 17 | empty |
| 3 | 81 | 0.39 | 0.77 | 20 | empty |
| 4 | 62 | 0.33 | 0.77 | 17 | CL |
Interfaces
1 interface between chains.
- A–B · 3052 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4QGP · Crystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at… · 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 O29089
- Elsewhere: RCSB PDB 4QGP · PDBe 4QGP · UniProt O29089
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