MolNFT v1 · #9298 · protein
The structure of the yrdc gene product from E.COLI
1HRU: “The structure of the yrdc gene product from E.COLI”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.61). MolNFT v1 #9298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HRU
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yrdc gene product
- UniProt
- P45748
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yrdc gene product | protein | 186 | 35% helix, 19% strand | P45748 |
| B | Yrdc gene product | protein | 184 | 35% helix, 18% strand | P45748 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.61 | 0.80 | 34 | empty |
| 2 | 191 | 0.55 | 0.79 | 31 | empty |
| 3 | 151 | 0.46 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
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 P45748
- Elsewhere: RCSB PDB 1HRU · PDBe 1HRU · UniProt P45748
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