MolNFT v2 · #156988 · protein
Crystal structure of HPSG
6LON · PFL2/glycerol dehydratase family glycyl radical enzyme: “Crystal structure of HPSG”. X-ray diffraction at 2.2, 2 ligands (LLQ, NA), 20 pockets (best druggability 0.83). MolNFT v2 #156988 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LON
- Type
- protein
- Length
- 3,214 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Bilophila wadsworthia 3_1_6
- Molecule
- PFL2/glycerol dehydratase family glycyl radical enzyme
- UniProt
- E5Y7I4
- Ligands
- LLQ, NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | PFL2/glycerol dehydratase family glycyl radical enzyme | protein | 802 | 52% helix, 10% strand | E5Y7I4 |
| A, C, D | PFL2/glycerol dehydratase family glycyl radical enzyme | protein | 804 | 53% helix, 10% strand | E5Y7I4 |
Ligands and binding sites
- LLQ · (2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid · ligand · 4 copies · chains B, A, C, D
- NA · Sodium ion · metal · 4 copies · chains B, A, C, D
- GOL · Glycerol · additive · 54 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.83 | 0.98 | 37 | GOL |
| 2 | 196 | 0.83 | 0.97 | 40 | GOL |
| 3 | 987 | 0.80 | 0.81 | 92 | GOL |
| 4 | 123 | 0.79 | 0.97 | 31 | GOL |
| 5 | 133 | 0.78 | 0.96 | 38 | empty |
Interfaces
4 interfaces between chains.
- B–A · 1379 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1376 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 989 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6LON · Crystal structure of hpsg · the same entry in another collection · 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 E5Y7I4
- Elsewhere: RCSB PDB 6LON · PDBe 6LON · UniProt E5Y7I4
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