Research workbench
Crystal structure of bacillus subtilis udp-glcnac 2-epimerase in complex with udp-glcnac and udp
Analyse Crystal structure of bacillus subtilis udp-glcnac 2-epimerase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FKZ
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 2-epimerase
- EC
- 5.1.3.14
- UniProt
- P39131
- Ligands
- UD1, UDP
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 384 | 47% helix, 15% strand | P39131 |
| B | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 376 | 48% helix, 16% strand | P39131 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.83 | 0.90 | 61 | UD1, UDP |
| 2 | 488 | 0.82 | 0.89 | 60 | UD1, UDP |
| 3 | 431 | 0.65 | 0.78 | 45 | empty |
| 4 | 61 | 0.31 | 0.75 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1399 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4FKZ · Crystal structure of Bacillus subtilis UDP-GlcNAc 2-epimerase in complex with UDP-GlcNAc… · the same entry in another collection · chain A against A, TM-score 1.00
- P39131 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 2-epimerase (P39131) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P39131
- Elsewhere: RCSB PDB 4FKZ · PDBe 4FKZ · UniProt P39131
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.