Research workbench
Crystal structure of escherichia COLI periplasmic glucose-1- phosphatase H18D mutant
Analyse Crystal structure of escherichia COLI periplasmic glucose-1- phosphatase H18D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RMR
- Type
- protein
- Length
- 774 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
- ZN
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-1-phosphatase (EC 3.1.3.10) | protein | 385 | 40% helix, 16% strand | P19926 |
| B | Glucose-1-phosphatase (EC 3.1.3.10) | protein | 389 | 42% helix, 16% strand | P19926 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · 16 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.68 | 0.80 | 50 | ACT, EDO |
| 2 | 70 | 0.62 | 0.91 | 26 | empty |
| 3 | 201 | 0.61 | 0.82 | 26 | ACT |
| 4 | 83 | 0.59 | 0.88 | 27 | ACT |
| 5 | 301 | 0.59 | 0.78 | 32 | 1PE, ACT |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6RMR · Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D 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 6RMR · PDBe 6RMR · UniProt P19926
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