MolNFT v1 · #170325 · protein
Crystal structure of the PBY1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (DCP1-DCP2-EDC3)
6Y3Z · M7GPPPN-mRNA hydrolase: “Crystal structure of the PBY1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex…”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.79). MolNFT v1 #170325 on GenesisL1: 3D…
- PDB
- 6Y3Z
- Type
- protein
- Length
- 672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M7GPPPN-mRNA hydrolase; MRNA-decapping enzyme subunit 1; Enhancer of mRNA-decapping…
- EC
- 3.6.1.62, 6.3.2.25
- UniProt
- P53550, Q12517, P39998, P38254
- Ligands
- MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M7GPPPN-mRNA hydrolase (EC 3.6.1.62) | protein | 243 | 44% helix, 19% strand | P53550 |
| B | MRNA-decapping enzyme subunit 1 | protein | 18 | 83% helix, 0% strand | Q12517 |
| C | Enhancer of mRNA-decapping protein 3 | protein | 63 | 5% helix, 57% strand | P39998 |
| P | Probable tubulin--tyrosine ligase PBY1 (EC 6.3.2.25) | protein | 348 | 35% helix, 23% strand | P38254 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.79 | 0.80 | 92 | empty |
| 2 | 447 | 0.71 | 0.82 | 32 | empty |
| 3 | 299 | 0.64 | 0.80 | 30 | empty |
| 4 | 169 | 0.54 | 0.79 | 27 | empty |
| 5 | 225 | 0.52 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–P · 1328 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 283 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y3Z · Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping… · the same entry in another collection · chain P against P, TM-score 1.00
- P38254 · AlphaFold monomer V2.0 prediction for probable tubulin--tyrosine ligase PBY1 (P38254) · a predicted model of the same protein · chain P against A, TM-score 0.93
- P39998 · AlphaFold monomer V2.0 prediction for enhancer of mRNA-decapping protein 3 (P39998) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P53550 · AlphaFold monomer V2.0 prediction for M7GPPPN-mRNA hydrolase (P53550) · a predicted model of the same protein · chain A against A, TM-score 0.65
- Q12517 · AlphaFold monomer V2.0 prediction for mRNA-decapping enzyme subunit 1 (Q12517) · a predicted model of the same protein · chain B against A, TM-score 0.37
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
- Every structure of UniProt Q12517
- Every structure of UniProt P39998
- Every structure of UniProt P38254
- Elsewhere: RCSB PDB 6Y3Z · PDBe 6Y3Z · UniProt P53550 · UniProt Q12517 · UniProt P39998 · UniProt P38254
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