MolNFT v1 · #141871 · protein
Crystal structure of udp-glcnac 2-epimerase neuc complexed with udp
5ZLT · GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing): “Crystal structure of udp-glcnac 2-epimerase neuc complexed with udp”. X-ray diffraction, 2 ligands (UDP, SO4), 15 pockets (best druggability 0.84). MolNFT v1 #141871 on…
- PDB
- 5ZLT
- Type
- protein
- Length
- 1,472 residues
- Chains
- 4
- 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, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing) (EC 3.2.1.184) | protein | 370 | 43% helix, 16% strand | A0A154EJU5 |
| B, D | GDP/UDP-N,N'-diacetylbacillosamine 2-epimerase (hydrolyzing) (EC 3.2.1.184) | protein | 366 | 44% helix, 16% strand | A0A154EJU5 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.84 | 0.91 | 56 | UDP |
| 2 | 435 | 0.82 | 0.90 | 57 | UDP |
| 3 | 975 | 0.80 | 0.82 | 80 | SO4 |
| 4 | 1028 | 0.80 | 0.82 | 90 | SO4 |
| 5 | 66 | 0.73 | 0.97 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2006 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1976 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 757 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 740 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ZLT · 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 5ZLT · PDBe 5ZLT · UniProt A0A154EJU5
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