Research workbench
Crystal structure of a nucleoside-diphosphate-sugar epimerase (SAV0421) from staphylococcus aureus, northeast structural genomics consortium target ZR319
Analyse Crystal structure of a nucleoside-diphosphate-sugar epimerase (SAV0421) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E48
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nucleoside-diphosphate-sugar epimerase
- UniProt
- Q99WI2
- Ligands
- MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nucleoside-diphosphate-sugar epimerase | protein | 279 | 46% helix, 19% strand | Q99WI2 |
| B | Putative nucleoside-diphosphate-sugar epimerase | protein | 289 | 44% helix, 18% strand | Q99WI2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.74 | 0.81 | 50 | empty |
| 2 | 598 | 0.72 | 0.79 | 50 | empty |
| 3 | 111 | 0.39 | 0.75 | 19 | empty |
| 4 | 95 | 0.38 | 0.76 | 19 | empty |
| 5 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3E48 · Crystal structure of a nucleoside-diphosphate-sugar epimerase (SAV0421) from… · 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 Q99WI2
- Elsewhere: RCSB PDB 3E48 · PDBe 3E48 · UniProt Q99WI2
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