Research workbench
Crystal structure of udp-glcnac 2-epimerase neuc complexed with udp
Analyse Crystal structure of udp-glcnac 2-epimerase neuc complexed with udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVS
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing)
- EC
- 3.2.1.184
- UniProt
- A0A154EJU5
- Ligands
- UDP, NAG, LI
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing) (EC 3.2.1.184) | protein | 359 | 45% helix, 16% strand | A0A154EJU5 |
| B | GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing) (EC 3.2.1.184) | protein | 366 | 45% helix, 16% strand | A0A154EJU5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- LI · Lithium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.80 | 0.87 | 70 | UDP, NAG |
| 2 | 1028 | 0.75 | 0.77 | 97 | UDP |
| 3 | 162 | 0.55 | 0.80 | 40 | empty |
| 4 | 104 | 0.52 | 0.83 | 25 | empty |
| 5 | 84 | 0.48 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1974 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5XVS · Crystal structure of UDP-GlcNAc 2-epimerase NeuC complexed with UDP · 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 A0A154EJU5
- Elsewhere: RCSB PDB 5XVS · PDBe 5XVS · UniProt A0A154EJU5
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