Research workbench
Bovine enterovirus F3 in complex with glutathione and a cysteinylglycine dipeptide
Analyse Bovine enterovirus F3 in complex with glutathione and a cysteinylglycine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T48
- Type
- protein
- Length
- 806 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q2LKZ0
- Ligands
- CYS, STE, GSH, GLY, K, SO4, CL
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 271 | 12% helix, 33% strand | Q2LKZ0 |
| B | VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 244 | 14% helix, 38% strand | Q2LKZ0 |
| C | VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 243 | 9% helix, 30% strand | Q2LKZ0 |
| D | VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 48 | 15% helix, 8% strand | Q2LKZ0 |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A, C
- STE · Stearic acid · ligand · chains A, C
- GSH · Glutathione · ligand · chains A, C
- GLY · Glycine · ligand · chains A, C
- K · Potassium ion · metal · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.84 | 0.93 | 47 | STE |
| 2 | 264 | 0.60 | 0.79 | 38 | K |
| 3 | 151 | 0.50 | 0.79 | 28 | empty |
| 4 | 138 | 0.46 | 0.77 | 34 | empty |
| 5 | 95 | 0.44 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3988 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 2152 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1668 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1339 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6T48 · Bovine enterovirus F3 in complex with glutathione and a Cysteinylglycine dipeptide · the same entry in another collection · chain D against D, 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 Q2LKZ0
- Elsewhere: RCSB PDB 6T48 · PDBe 6T48 · UniProt Q2LKZ0
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