Research workbench
Crystal structure of yedp, phosphatase-like domain protein from escherichia COLI K12
Analyse Crystal structure of yedp, phosphatase-like domain protein from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XVI
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mannosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.70
- UniProt
- P76329
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 232 | 40% helix, 20% strand | P76329 |
| B | Putative mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 234 | 39% helix, 21% strand | P76329 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.70 | 0.83 | 49 | SO4 |
| 2 | 408 | 0.65 | 0.79 | 45 | SO4 |
| 3 | 182 | 0.51 | 0.77 | 21 | empty |
| 4 | 172 | 0.49 | 0.76 | 20 | empty |
| 5 | 94 | 0.43 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 294 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1XVI · Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12 · the same entry in another collection · chain A against A, TM-score 1.00
- P76329 · AlphaFold monomer V2.0 prediction for mannosyl-3-phosphoglycerate phosphatase (P76329) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P76329
- Elsewhere: RCSB PDB 1XVI · PDBe 1XVI · UniProt P76329
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