Research workbench
Cryoem structure of DNA polymerase alpha - primase bound to SARS cov NSP1
Analyse Cryoem structure of DNA polymerase alpha - primase bound to SARS cov NSP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPL
- Type
- protein
- Length
- 2,442 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha catalytic subunit; DNA polymerase alpha subunit B; DNA primase small…
- EC
- 2.7.7.7, 2.7.7.-
- UniProt
- P09884, Q14181, P49642, P49643, P0C6U8
- Ligands
- SF4, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase alpha catalytic subunit (EC 2.7.7.7) | protein | 1070 | 39% helix, 17% strand | P09884 |
| B | DNA polymerase alpha subunit B | protein | 444 | 21% helix, 23% strand | Q14181 |
| C | DNA primase small subunit (EC 2.7.7.-) | protein | 389 | 50% helix, 11% strand | P49642 |
| D | DNA primase large subunit | protein | 434 | 61% helix, 3% strand | P49643 |
| E | Non-structural protein 1 | protein | 105 | 19% helix, 32% strand | P0C6U8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.84 | 0.90 | 63 | empty |
| 2 | 864 | 0.83 | 0.85 | 88 | empty |
| 3 | 311 | 0.79 | 0.90 | 61 | empty |
| 4 | 106 | 0.78 | 0.97 | 26 | empty |
| 5 | 176 | 0.78 | 0.93 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2977 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2776 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 746 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 744 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7OPL · CryoEM structure of DNA Polymerase alpha - primase bound to SARS CoV nsp1 · the same entry in another collection · chain E against E, TM-score 1.00
- P49642 · AlphaFold monomer V2.0 prediction for DNA primase small subunit (P49642) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q14181 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha subunit B (Q14181) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P49643 · AlphaFold monomer V2.0 prediction for DNA primase large subunit (P49643) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P09884 · AlphaFold monomer V2.0 prediction for DNA polymerase alpha catalytic subunit (P09884) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P09884
- Every structure of UniProt Q14181
- Every structure of UniProt P49642
- Every structure of UniProt P49643
- Every structure of UniProt P0C6U8
- Elsewhere: RCSB PDB 7OPL · PDBe 7OPL · UniProt P09884 · UniProt Q14181 · UniProt P49642 · UniProt P49643 · UniProt P0C6U8
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