Research workbench
Crystal structure of saccharomyces cerevisiae DCP2 nudix domain (E198Q mutation)
Analyse Crystal structure of saccharomyces cerevisiae DCP2 nudix domain (E198Q mutation) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KG4
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-decapping enzyme subunit 2
- EC
- 3.-.-.-
- UniProt
- P53550
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-decapping enzyme subunit 2 (EC 3.-.-.-) | protein | 138 | 27% helix, 31% strand | P53550 |
| B | MRNA-decapping enzyme subunit 2 (EC 3.-.-.-) | protein | 141 | 23% helix, 35% strand | P53550 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.52 | 0.75 | 42 | empty |
| 2 | 74 | 0.35 | 0.77 | 19 | empty |
| 3 | 88 | 0.34 | 0.74 | 17 | empty |
| 4 | 50 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KG4 · Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain (E198Q mutation) · the same entry in another collection · chain A against A, TM-score 1.00
- P53550 · AlphaFold monomer V2.0 prediction for M7GPPPN-mRNA hydrolase (P53550) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P53550
- Elsewhere: RCSB PDB 4KG4 · PDBe 4KG4 · UniProt P53550
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