Research workbench
Crystal structure of a putative metal dependent phosphohydrolase (SAG1661) from streptococcus agalactiae serogroup V at 1.85 a resolution
Analyse Crystal structure of a putative metal dependent phosphohydrolase (SAG1661) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGI
- Type
- protein
- Length
- 387 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein SAG1661
- UniProt
- Q8DY32
- Ligands
- GDP, FE, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein SAG1661 | protein | 193 | 69% helix, 0% strand | Q8DY32 |
| B | Hypothetical protein SAG1661 | protein | 194 | 69% helix, 0% strand | Q8DY32 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.60 | 0.78 | 33 | FE, GDP |
| 2 | 289 | 0.59 | 0.78 | 29 | FE, GDP |
Interfaces
1 interface between chains.
- A–B · 565 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 2OGI · Crystal structure of a putative metal dependent phosphohydrolase (sag1661) from… · 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 Q8DY32
- Elsewhere: RCSB PDB 2OGI · PDBe 2OGI · UniProt Q8DY32
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