MolNFT v1 · #25142 · protein
Crystal structure of udp-N-ACETYLGLUCOSAMINE_2 epimerase
1VGV · Udp-N-acetylglucosamine 2-epimerase: “Crystal structure of udp-N-ACETYLGLUCOSAMINE_2 epimerase”. X-ray diffraction, 1 ligand (UD1), 17 pockets (best druggability 0.78). MolNFT v1 #25142 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1VGV
- 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
- UD1
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 376 | 48% helix, 16% strand | P27828 |
| B | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 372 | 49% helix, 15% strand | P27828 |
| C | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 367 | 50% helix, 14% strand | P27828 |
| D | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 374 | 45% helix, 15% strand | P27828 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.78 | 0.81 | 80 | UD1 |
| 2 | 701 | 0.74 | 0.80 | 56 | UD1 |
| 3 | 915 | 0.72 | 0.77 | 81 | empty |
| 4 | 772 | 0.71 | 0.77 | 67 | empty |
| 5 | 635 | 0.69 | 0.77 | 58 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1612 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1601 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 626 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 75 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 1VGV · Crystal structure of UDP-N-acetylglucosamine_2 epimerase · 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 1VGV · PDBe 1VGV · UniProt P27828
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