Research workbench
Cryo-EM structure of PCV2 replicase bound to ssdna
Analyse Cryo-EM structure of PCV2 replicase bound to ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LAR
- Type
- protein + DNA
- Length
- 1,104 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent helicase rep; DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.6.4.-
- UniProt
- Q6TC59
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | ATP-dependent helicase rep (EC 3.6.4.-) | protein | 183 | 30% helix, 21% strand | Q6TC59 |
| G | DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.88 | 0.89 | 127 | empty |
| 2 | 544 | 0.76 | 0.83 | 58 | empty |
| 3 | 187 | 0.68 | 0.87 | 28 | empty |
| 4 | 179 | 0.68 | 0.87 | 29 | empty |
| 5 | 761 | 0.67 | 0.75 | 59 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1424 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1406 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1406 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1397 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1383 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7LAR · Cryo-EM structure of PCV2 Replicase bound to ssDNA · 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 Q6TC59
- Elsewhere: RCSB PDB 7LAR · PDBe 7LAR · UniProt Q6TC59
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