Research workbench
Yeast scavenger decapping enzyme in complex with M7GDP
Analyse Yeast scavenger decapping enzyme in complex with M7GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BV3
- Type
- protein
- Length
- 1,289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M7GPPPX diphosphatase
- EC
- 3.6.1.59
- UniProt
- Q06151
- Ligands
- M7G, SO4, CL
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 329 | 30% helix, 29% strand | Q06151 |
| B | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 316 | 33% helix, 29% strand | Q06151 |
| C | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 333 | 31% helix, 30% strand | Q06151 |
| D | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 311 | 32% helix, 30% strand | Q06151 |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, C, D
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 | 968 | 0.87 | 0.89 | 91 | M7G, SO4 |
| 2 | 1048 | 0.86 | 0.87 | 95 | M7G, SO4, CL |
| 3 | 123 | 0.79 | 0.97 | 33 | empty |
| 4 | 111 | 0.78 | 0.97 | 31 | empty |
| 5 | 621 | 0.72 | 0.79 | 72 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 5956 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 5872 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 328 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q06151
- Elsewhere: RCSB PDB 5BV3 · PDBe 5BV3 · UniProt Q06151
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