Research workbench
Crystal structure of glycerol phosphate phosphatase RV1692 from mycobacterium tuberculosis in complex with magnesium
Analyse Crystal structure of glycerol phosphate phosphatase RV1692 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9G
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol 3-phosphate phosphatase
- UniProt
- O33194
- Ligands
- MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol 3-phosphate phosphatase | protein | 329 | 36% helix, 23% strand | O33194 |
| B | Glycerol 3-phosphate phosphatase | protein | 326 | 37% helix, 22% strand | O33194 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, 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 | 349 | 0.66 | 0.80 | 39 | MG |
| 2 | 360 | 0.64 | 0.79 | 38 | MG |
Interfaces
1 interface between chains.
- A–B · 1142 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4I9G · Crystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- O33194 · AlphaFold monomer V2.0 prediction for D-glycerol 3-phosphate phosphatase (O33194) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O33194
- Elsewhere: RCSB PDB 4I9G · PDBe 4I9G · UniProt O33194
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