MolNFT v1 · #6234 · protein
The structure of udp-N-acetylglucosamine 2-epimerase from E. COLI.
1F6D: “The structure of udp-N-acetylglucosamine 2-epimerase from E. COLI.”. X-ray diffraction, 3 ligands (UDP, NA, CL), 16 pockets (best druggability 0.76). MolNFT v1 #6234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F6D
- Type
- protein
- Length
- 1,489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 2-epimerase
- EC
- 5.1.3.14
- UniProt
- P27828
- Ligands
- UDP, NA, CL
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 376 | 48% helix, 15% strand | P27828 |
| B | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 372 | 45% helix, 15% strand | P27828 |
| C | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 367 | 45% helix, 14% strand | P27828 |
| D | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 374 | 49% helix, 14% strand | P27828 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.76 | 0.80 | 70 | UDP |
| 2 | 869 | 0.75 | 0.79 | 73 | UDP |
| 3 | 902 | 0.73 | 0.77 | 77 | UDP |
| 4 | 743 | 0.71 | 0.77 | 72 | UDP |
| 5 | 158 | 0.61 | 0.84 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1615 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 1F6D · The structure of udp-N-acetylglucosamine 2-epimerase from E. COLI. · the same entry in another collection · chain D against D, TM-score 1.00
- P27828 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 2-epimerase (P27828) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P27828
- Elsewhere: RCSB PDB 1F6D · PDBe 1F6D · UniProt P27828
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.