Research workbench
Structure of primase-helicase in SAPI5
Analyse Structure of primase-helicase in SAPI5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OLA
- Type
- protein
- Length
- 2,394 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase
- UniProt
- A0A1S5ZIL8
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase | protein | 445 | 38% helix, 14% strand | A0A1S5ZIL8 |
| B | DNA primase | protein | 446 | 37% helix, 14% strand | A0A1S5ZIL8 |
| C | DNA primase | protein | 431 | 40% helix, 13% strand | A0A1S5ZIL8 |
| D | DNA primase | protein | 375 | 38% helix, 14% strand | A0A1S5ZIL8 |
| E | DNA primase | protein | 349 | 35% helix, 15% strand | A0A1S5ZIL8 |
| F | DNA primase | protein | 348 | 36% helix, 15% strand | A0A1S5ZIL8 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, F, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
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 | 985 | 0.86 | 0.87 | 112 | empty |
| 2 | 1059 | 0.79 | 0.80 | 101 | ANP, MG |
| 3 | 620 | 0.79 | 0.84 | 74 | empty |
| 4 | 582 | 0.79 | 0.85 | 55 | ANP |
| 5 | 200 | 0.76 | 0.91 | 33 | ANP, MG |
Interfaces
6 interfaces between chains.
- B–C · 2059 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2020 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1954 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1653 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1597 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7OLA · Structure of Primase-Helicase in SaPI5 · the same entry in another collection · chain B against B, 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 7OLA · PDBe 7OLA · UniProt A0A1S5ZIL8
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