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
- 7LAS
- Type
- protein + DNA
- Length
- 1,122 residues
- Chains
- 8
- 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*CP*GP*AP*TP*CP*GP*AP*TP*C)-3')…
- EC
- 3.6.4.-
- UniProt
- Q6TC59
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 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*CP*GP*AP*TP*CP*GP*AP*TP*C)-3') | dna | 14 | — | — |
| H | DNA (5'-D(P*GP*AP*TP*CP*GP*AP*TP*CP*GP*A)-3') | dna | 10 | — | — |
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 | 676 | 0.85 | 0.89 | 85 | empty |
| 2 | 820 | 0.81 | 0.84 | 78 | empty |
| 3 | 475 | 0.75 | 0.84 | 49 | empty |
| 4 | 155 | 0.74 | 0.92 | 30 | empty |
| 5 | 195 | 0.70 | 0.88 | 30 | empty |
Interfaces
16 interfaces between chains.
- D–E · 1425 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1407 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1346 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7LAS · 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 7LAS · PDBe 7LAS · UniProt Q6TC59
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