MolNFT v1 · #184318 · protein
Structure of primase-helicase in SAPI5
7OM0 · DNA primase: “Structure of primase-helicase in SAPI5”. Electron microscopy, 1 ligand (ANP), 20 pockets (best druggability 0.77). MolNFT v1 #184318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OM0
- Type
- protein
- Length
- 2,657 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase
- UniProt
- A0A1S5ZIL8
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, E, C | DNA primase | protein | 443 | 38% helix, 14% strand | A0A1S5ZIL8 |
| D | DNA primase | protein | 442 | 38% helix, 13% strand | A0A1S5ZIL8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.77 | 0.82 | 97 | empty |
| 2 | 550 | 0.77 | 0.83 | 80 | empty |
| 3 | 306 | 0.76 | 0.88 | 48 | ANP |
| 4 | 313 | 0.76 | 0.88 | 46 | ANP |
| 5 | 907 | 0.75 | 0.79 | 88 | empty |
Interfaces
6 interfaces between chains.
- F–E · 2035 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 2020 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2019 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2013 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2002 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7OM0 · Structure of Primase-Helicase in SaPI5 · 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 A0A1S5ZIL8
- Elsewhere: RCSB PDB 7OM0 · PDBe 7OM0 · UniProt A0A1S5ZIL8
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