MolNFT v1 · #113250 · protein
Structural basis for DNA strand separation by a hexameric replicative helicase
5A9K · Replication protein E1: “Structural basis for DNA strand separation by a hexameric replicative helicase”. Electron microscopy, 2 ligands (MG, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #113250 on GenesisL1: 3D structure…
- PDB
- 5A9K
- Type
- protein
- Length
- 1,620 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication protein E1
- EC
- 3.6.4.12
- UniProt
- P03116
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication protein E1 (EC 3.6.4.12) | protein | 272 | 49% helix, 10% strand | P03116 |
| B | Replication protein E1 (EC 3.6.4.12) | protein | 268 | 51% helix, 10% strand | P03116 |
| C | Replication protein E1 (EC 3.6.4.12) | protein | 267 | 54% helix, 10% strand | P03116 |
| D | Replication protein E1 (EC 3.6.4.12) | protein | 274 | 52% helix, 10% strand | P03116 |
| E | Replication protein E1 (EC 3.6.4.12) | protein | 270 | 54% helix, 11% strand | P03116 |
| F | Replication protein E1 (EC 3.6.4.12) | protein | 269 | 51% helix, 11% strand | P03116 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.82 | 0.85 | 90 | empty |
| 2 | 985 | 0.82 | 0.83 | 100 | PO4, MG |
| 3 | 773 | 0.80 | 0.83 | 74 | empty |
| 4 | 386 | 0.73 | 0.84 | 38 | empty |
| 5 | 65 | 0.69 | 0.96 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1993 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1927 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1853 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1838 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1696 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5A9K · Structural basis for DNA strand separation by a hexameric replicative helicase · 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 P03116
- Elsewhere: RCSB PDB 5A9K · PDBe 5A9K · UniProt P03116
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