Research workbench
Crystal structure of S. pombe DCP1/DCP2 in complex with H. sapiens PNRC2
Analyse Crystal structure of S. pombe DCP1/DCP2 in complex with H. sapiens PNRC2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KQ1
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-decapping enzyme subunit 1; Proline-rich nuclear receptor coactivator 2; MRNA…
- EC
- 3.-.-.-
- UniProt
- Q9P805, Q9NPJ4, O13828
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-decapping enzyme subunit 1 | protein | 126 | 28% helix, 48% strand | Q9P805 |
| C | Proline-rich nuclear receptor coactivator 2 | protein | 22 | 14% helix, 0% strand | Q9NPJ4 |
| B | MRNA decapping complex subunit 2 (EC 3.-.-.-) | protein | 236 | 41% helix, 19% strand | O13828 |
| D | MRNA-decapping enzyme subunit 1 | protein | 122 | 25% helix, 49% strand | Q9P805 |
| F | Proline-rich nuclear receptor coactivator 2 | protein | 21 | 0% helix, 0% strand | Q9NPJ4 |
| E | MRNA decapping complex subunit 2 (EC 3.-.-.-) | protein | 235 | 39% helix, 20% strand | O13828 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.74 | 0.78 | 103 | empty |
| 2 | 353 | 0.61 | 0.78 | 42 | empty |
| 3 | 63 | 0.50 | 0.85 | 12 | empty |
| 4 | 90 | 0.48 | 0.82 | 18 | empty |
| 5 | 98 | 0.41 | 0.77 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1139 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1102 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 857 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 804 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 293 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5KQ1 · Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 · the same entry in another collection · chain E against E, TM-score 1.00
- Q9P805 · AlphaFold monomer V2.0 prediction for mRNA-decapping enzyme subunit 1 (Q9P805) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O13828 · AlphaFold monomer V2.0 prediction for mRNA decapping complex subunit 2 (O13828) · a predicted model of the same protein · chain E against A, TM-score 0.60
- Q9NPJ4 · AlphaFold monomer V2.0 prediction for proline-rich nuclear receptor coactivator 2 (Q9NPJ4) · a predicted model of the same protein · chain C against A, TM-score 0.48
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 Q9P805
- Every structure of UniProt Q9NPJ4
- Every structure of UniProt O13828
- Elsewhere: RCSB PDB 5KQ1 · PDBe 5KQ1 · UniProt Q9P805 · UniProt Q9NPJ4 · UniProt O13828
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