Research workbench
Crystal structure of apo form of D,D-heptose 1.7-bisphosphate phosphatase from E. COLI
Analyse Crystal structure of apo form of D,D-heptose 1.7-bisphosphate phosphatase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L8E
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D,D-heptose 1,7-bisphosphate phosphatase
- EC
- 3.1.3.-
- UniProt
- P63228
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D,D-heptose 1,7-bisphosphate phosphatase (EC 3.1.3.-) | protein | 185 | 39% helix, 19% strand | P63228 |
| B | D,D-heptose 1,7-bisphosphate phosphatase (EC 3.1.3.-) | protein | 183 | 41% helix, 19% strand | P63228 |
Ligands and binding sites
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 | 615 | 0.72 | 0.80 | 70 | ACY |
Interfaces
1 interface between chains.
- A–B · 816 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3L8E · Crystal Structure of apo form of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli · the same entry in another collection · chain A against A, TM-score 1.00
- P63228 · AlphaFold monomer V2.0 prediction for D-glycero-beta-D-manno- heptose-1,7-bisphosphate… · 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 P63228
- Elsewhere: RCSB PDB 3L8E · PDBe 3L8E · UniProt P63228
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