Research workbench
Mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
Analyse Mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F1Y
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Rubrobacter xylanophilus; synthetic construct
- Molecule
- Mannosyl-3-phosphoglycerate synthase
- EC
- 2.4.1.217
- UniProt
- B7SY86
- Ligands
- MG, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 318 | 42% helix, 20% strand | B7SY86 |
| C | Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) | protein | 318 | 43% helix, 20% strand | B7SY86 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.74 | 0.81 | 61 | empty |
| 2 | 647 | 0.73 | 0.80 | 60 | empty |
| 3 | 84 | 0.56 | 0.86 | 20 | empty |
| 4 | 62 | 0.40 | 0.80 | 17 | MG |
Interfaces
1 interface between chains.
- A–C · 3158 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3F1Y · Mannosyl-3-phosphoglycerate synthase from rubrobacter xylanophilus · the same entry in another collection · chain A against A, TM-score 1.00
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 B7SY86
- Elsewhere: RCSB PDB 3F1Y · PDBe 3F1Y · UniProt B7SY86
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