Research workbench
Crystal structure of putative mannac-6-P epimerase from staphylococcus aureus (strain N315)
Analyse Crystal structure of putative mannac-6-P epimerase from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y0E
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylmannosamine-6-phosphate 2-epimerase
- EC
- 5.1.3.9
- UniProt
- P65517
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9) | protein | 222 | 41% helix, 17% strand | P65517 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.61 | 0.80 | 27 | PO4 |
| 2 | 214 | 0.57 | 0.80 | 24 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1554 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1Y0E · Crystal structure of putative ManNAc-6-P epimerase from Staphylococcus aureus (strain… · the same entry in another collection · chain A against A, TM-score 1.00
- P65517 · AlphaFold monomer V2.0 prediction for putative N-acetylmannosamine-6-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P65517
- Elsewhere: RCSB PDB 1Y0E · PDBe 1Y0E · UniProt P65517
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