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Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from lactobacillus delbrueckii subsp. bulgaricus atcc baa-365 at 1.51 a resolution
Analyse Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HI0
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphoglycolate phosphatase
- EC
- 3.1.3.18
- UniProt
- Q1GA24
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phosphoglycolate phosphatase (EC 3.1.3.18) | protein | 240 | 47% helix, 15% strand | Q1GA24 |
| B | Putative phosphoglycolate phosphatase (EC 3.1.3.18) | protein | 239 | 47% helix, 16% strand | Q1GA24 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.76 | 0.78 | 93 | NA, CL, EDO |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2HI0 · Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) 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 Q1GA24
- Elsewhere: RCSB PDB 2HI0 · PDBe 2HI0 · UniProt Q1GA24
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