Research workbench
S.C. scavenger decapping enzyme dcps in complex with the capped RNA dinucleotide M7G-gu
Analyse S.C. scavenger decapping enzyme dcps in complex with the capped RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TRQ
- Type
- protein
- Length
- 1,309 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
- 2PO, U, 0G, M7G, SO4
- Pockets
- 20 · best druggability 0.86
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 | 332 | 30% helix, 29% strand | Q06151 |
| B | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 323 | 32% helix, 30% strand | Q06151 |
| C | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 336 | 31% helix, 28% strand | Q06151 |
| D | M7GPPPX diphosphatase (EC 3.6.1.59) | protein | 318 | 31% helix, 29% strand | Q06151 |
Ligands and binding sites
- 2PO · Phosphonate · ligand · 2 copies · chains A, C
- U · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- 0G · L-guanosine-5'-monophosphate · ligand · 2 copies · chains A, C
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.86 | 0.88 | 73 | 2PO, U, 0G, M7G |
| 2 | 947 | 0.86 | 0.87 | 71 | U, 2PO, 0G, M7G |
| 3 | 182 | 0.83 | 0.97 | 33 | empty |
| 4 | 160 | 0.82 | 0.97 | 32 | empty |
| 5 | 930 | 0.76 | 0.78 | 75 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6013 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 5851 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 596 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 575 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 479 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6TRQ · S.c. Scavenger Decapping Enzyme DcpS in complex with the capped RNA dinucleotide m7G-GU · the same entry in another collection · chain D against D, TM-score 1.00
- Q06151 · AlphaFold monomer V2.0 prediction for M7GPPPX diphosphatase (Q06151) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6TRQ · PDBe 6TRQ · UniProt Q06151
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