MolNFT v1 · #72253 · protein
Crystal structure of yage, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. COLI K12 in complex with pyruvate
3N2X · Uncharacterized protein yage: “Crystal structure of yage, a prophage protein belonging to the dihydrodipicolinic acid synthase family from…”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #72253 on GenesisL1: 3D…
- PDB
- 3N2X
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein yage
- UniProt
- P75682
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein yage | protein | 298 | 51% helix, 12% strand | P75682 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.71 | 0.91 | 34 | empty |
| 2 | 177 | 0.69 | 0.88 | 40 | empty |
| 3 | 228 | 0.59 | 0.80 | 34 | empty |
| 4 | 251 | 0.59 | 0.79 | 39 | empty |
| 5 | 245 | 0.58 | 0.79 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1713 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1709 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 981 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 979 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 3N2X · Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- P75682 · AlphaFold monomer V2.0 prediction for putative 2-dehydro-3-deoxy-D- gluconate aldolase… · a predicted model of the same protein · 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 P75682
- Elsewhere: RCSB PDB 3N2X · PDBe 3N2X · UniProt P75682
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.