Research workbench
S. aureus mnaa-udp co-structure
Analyse S. aureus mnaa-udp co-structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ENZ
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glcnac 2-epimerase
- EC
- 5.1.3.14
- UniProt
- Q9REV4
- Ligands
- UDP, SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glcnac 2-epimerase (EC 5.1.3.14) | protein | 365 | 49% helix, 16% strand | Q9REV4 |
| B | Udp-glcnac 2-epimerase (EC 5.1.3.14) | protein | 373 | 48% helix, 16% strand | Q9REV4 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.79 | 0.84 | 60 | UDP, SO4, TRS |
| 2 | 517 | 0.74 | 0.82 | 55 | UDP, TRS |
| 3 | 348 | 0.68 | 0.81 | 47 | PG4 |
Interfaces
1 interface between chains.
- A–B · 1430 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5ENZ · S. aureus MnaA-UDP co-structure · 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 Q9REV4
- Elsewhere: RCSB PDB 5ENZ · PDBe 5ENZ · UniProt Q9REV4
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