MolNFT v1 · #125962 · protein
Structure of the active form of /K. lactis/ DCP1-DCP2-EDC3 decapping complex bound to M7GDP
5LOP · KLLA0F23980P: “Structure of the active form of /K. lactis/ DCP1-DCP2-EDC3 decapping complex bound to M7GDP”. X-ray diffraction, 2 ligands (M7G, MG), 6 pockets (best druggability 0.73). MolNFT v1 #125962 on GenesisL1: 3D structure…
- PDB
- 5LOP
- Type
- protein
- Length
- 494 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KLLA0F23980P; KLLA0E01827P; KLLA0A11308P
- UniProt
- Q6CIU1, Q6CPV9, Q6CX48
- Ligands
- M7G, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KLLA0F23980P | protein | 259 | 45% helix, 15% strand | Q6CIU1 |
| B | KLLA0E01827P | protein | 173 | 21% helix, 32% strand | Q6CPV9 |
| C | KLLA0A11308P | protein | 62 | 5% helix, 58% strand | Q6CX48 |
Ligands and binding sites
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.73 | 0.78 | 72 | MG, M7G |
| 2 | 203 | 0.62 | 0.82 | 27 | empty |
| 3 | 69 | 0.58 | 0.89 | 17 | empty |
| 4 | 97 | 0.48 | 0.81 | 17 | empty |
| 5 | 72 | 0.41 | 0.79 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1607 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 615 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LOP · Structure of the active form of /K. lactis/ Dcp1-Dcp2-Edc3 decapping complex bound to… · 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 Q6CIU1
- Every structure of UniProt Q6CPV9
- Every structure of UniProt Q6CX48
- Elsewhere: RCSB PDB 5LOP · PDBe 5LOP · UniProt Q6CIU1 · UniProt Q6CPV9 · UniProt Q6CX48
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