Research workbench
Crystal structure of escherichia COLI periplasmic glucose-1- phosphatase H18A mutant complexed with glucose-1-phosphate
Analyse Crystal structure of escherichia COLI periplasmic glucose-1- phosphatase H18A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NT4
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-1-phosphatase
- EC
- 3.1.3.10
- UniProt
- P19926
- Ligands
- XGP
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose-1-phosphatase (EC 3.1.3.10) | protein | 391 | 40% helix, 15% strand | P19926 |
Ligands and binding sites
- XGP · 1-O-phosphono-beta-D-glucopyranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.63 | 0.82 | 40 | XGP |
| 2 | 260 | 0.62 | 0.80 | 34 | XGP |
| 3 | 174 | 0.46 | 0.75 | 21 | empty |
| 4 | 63 | 0.41 | 0.81 | 14 | empty |
| 5 | 84 | 0.40 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1NT4 · Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18A mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P19926 · AlphaFold monomer V2.0 prediction for glucose-1-phosphatase (P19926) · a predicted model of the same protein · chain A 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 P19926
- Elsewhere: RCSB PDB 1NT4 · PDBe 1NT4 · UniProt P19926
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